Genetically modified lactate-consuming yeasts and fermentation processes using such genetically modified yeasts

ABSTRACT

The present invention relates to genetically modified yeasts that can use lactate as a carbon source to produce a fermentation product. In one aspect, the yeasts can consume glucose and lactate simultaneously to produce ethanol. In one aspect, the genetically modified yeast is transformed to include a monocarboxylic/monocarboxylate transporter. In one aspect, the yeast can include one or more heterologous genes encoding lactate dehydrogenase (cytochrome) (EC 1.1.2.3 and/or 1.1.2.4).

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Patent Application Ser. No. 62/395,792, filed Sep. 16, 2016, entitled “GENETICALLY MODIFIED LACTATE-CONSUMING YEASTS AND FERMENTATION PROCESSES USING SUCH GENETICALLY MODIFIED YEASTS”, which is hereby incorporated by reference herein in its entirety.

SEQUENCE LISTING

The entire contents of the ASCII text file entitled “N00478_ST25.txt,” created on Sep. 15, 2017, and having a size of 506 kilobytes, is incorporated herein by reference in its entirety.

BACKGROUND OF THE INVENTION

Industrial yeast fermentation processes often use corn process streams, for example corn steepwater, as a fermentation substrate. These process streams contain starches that can be converted to sugars via treatment with saccharification enzymes. In current fermentation processes, glucose or other sugars serve as the carbon source for fermentation. However, such process streams can contain a significant amount of lactate which cannot be efficiently used as a carbon source by yeasts, especially in the presence of glucose.

SUMMARY OF THE INVENTION

Described herein are genetically modified yeasts that can consume lactate during fermentation. In one aspect, the yeasts can use lactate as a carbon source to form a fermentation product. In one aspect, the yeasts can consume lactate and glucose simultaneously during a fermentation process to produce a fermentation product. In some embodiments, the fermentation product is ethanol (EtOH). In some embodiments, the yeast is a genetically modified Saccharomyces cerevisiae yeast. In some embodiments, the yeast is transformed to express a heterologous monocarboxylate/proton symporter, e.g., a JEN1 symporter. In some embodiments, the yeast is transformed to express one or more heterologous genes encoding a lactate dehydrogenase (cytochrome) (EC 1.1.2.3 or 1.1.2.4).

In one aspect, the genetically modified yeast comprises a heterologous gene encoding a monocarboxylic/monocarboxylate transporter and one or more heterologous genes encoding lactate dehydrogenase (cytochrome) (classified as EC 1.1.2.3 or 1.1.2.4), wherein the yeast is capable of consuming lactate and producing ethanol when the yeast is present in a fermentation medium comprising lactate and hexose. In some embodiments, the yeast is capable of consuming D-lactate, L-lactate, or a mixture thereof. In some embodiments, the yeast is capable of consuming both D-lactate and L-lactate. In some embodiments, the yeast has a L-lactate consumption rate of at least 0.030, 0.035, 0.040, 0.045, or 0.050 g L⁻¹h⁻¹ when the concentration of hexose in the fermentation medium is 150 g/L or greater. In some embodiments, the yeast has a L-lactate consumption rate of at least 0.015, 0.020, 0.025, 0.030, 0.035, or 0.040 gL⁻¹h⁻¹ when the concentration of hexose in the fermentation medium is 5 g/L or greater. In some embodiments, the yeast has a D-lactate consumption rate of at least 0.005, 0.006, 0.007, 0.008, 0.009, 0.010, 0.015, 0.020, 0.025, or 0.030 gL⁻¹h⁻¹ when the concentration of hexose in the fermentation medium is 150 g/L or greater. In some embodiments, the yeast has a D-lactate consumption rate of at least 0.015, 0.020, 0.025, 0.030, 0.035, or 0.040 gL⁻¹h⁻¹ when the concentration of hexose in the fermentation medium is 5 g/L or greater. In some embodiments, the lactate consumption rate of D-lactate, L-lactate, or total lactate for the yeast is determined according to the “Evaluation Protocol for Lactate Consumption” described later herein.

In some embodiments, the yeast has a total lactate consumption rate (i.e., consumption of both D- and L-lactate) of at least 0.550, 0.555, 0.600 or 0.650 gL⁻¹h⁻¹ between time 0 and 7 hours in a simultaneous saccharification fermentation (SSF) process. In some embodiments, the yeast has a total lactate consumption rate of at least 0.130, 0.140, 0.150, 0.160, or 0.170 gL⁻¹h⁻¹ between time 7 hours and 48 hours in a SSF process. In some embodiments, the yeast has a total lactate consumption rate of at least 0.200, 0.210, 0.220, 0.230, 0.240, or 0.250 gL⁻¹h⁻¹ between time 0 and 48 hours in a SSF process. In some embodiments, the total lactate consumption rate is determined according to the method for SSF shake flask assay in Example 4 described later herein.

In one aspect, the one or more heterologous lactate dehydrogenase (cytochrome) genes comprise an overexpressed D-lactate dehydrogenase (DLD) gene (EC 1.1.2.4). In one aspect, the one or more heterologous lactate dehydrogenase (cytochrome) genes comprise an overexpressed cytochrome b2 (CYB2) gene (EC 1.1.2.3). In some embodiments, the one or more heterologous lactate dehydrogenase (cytochrome) genes comprise an overexpressed DLD gene and an overexpressed CYB2 gene. In some embodiments, the one or more DLD genes is from the yeast genus of Saccharomyces, Issatchenkia, and/or Kluyveromyces. In some embodiments, the one or more DLD genes encodes for a DLD polypeptide having an amino acid sequence with a sequence identity of at least 90 or 95% to the DLD polypeptide from one or more of the following yeast species: Saccharomyces cerevisiae, Issatchenkia orientalis, Saccharyomyces kluyveri, Saccharyomyces bayanus, Kluyveromyces dobzhanskii, Kluyveromyces marxianus, or Kluyveromyces lactis. In some embodiments, the yeast encodes for a polypeptide having an amino acid sequence with a sequence identity of at least 50%, 55%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, or 99% to any one of the following amino acid sequences: SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 72, or SEQ ID NO: 74.

In some embodiments, the one or more CYB2 genes is from the yeast genus of Saccharomyces, Issatchenkia, Zygosaccharomyces, and/or Kluyveromyces. In some embodiments, the one or more CYB2 genes encodes for a CYB2 polypeptide having an amino acid sequence with a sequence identity of at least 90 or 95% to the CYB2 polypeptide from one or more of the following yeast species: Saccharomyces cerevisiae, Issatchenkia orientalis, Saccharyomyces kluyveri, Saccharyomyces bayanus, Zygosaccharomyces rouxii, Kluyveromyces dobzhanskii, or Kluyveromyces lactis. In some embodiments, the yeast encodes for a polypeptide having an amino acid sequence with a sequence identity of at least 50%, 55%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, or 99% to any one of the following amino acid sequences: SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, or SEQ ID NO: 62.

In one aspect, the yeast comprises heterologous genes other than a DLD, a CYB2, or a heterologous monocarboxylate/proton symporter. In some embodiments, the yeast comprises a heterologous gene encoding a lactate racemase.

In one aspect, the genetically modified yeast comprises a heterologous gene encoding a monocarboxylate/proton symporter (JEN1) and a heterologous gene encoding glucoamylase, wherein the yeast is capable of consuming lactate and producing ethanol when the yeast is present in a fermentation medium comprising lactate, and further comprising hexose, starch, or a combination thereof. In one aspect, any of the above yeasts be transformed with a heterologous glucoamylase gene. In some embodiments, the yeast can encode for a glucoamylase from Saccharomycopsis fibuligera or Rhizopus oryzae. In some embodiments, the yeast encodes for a glucoamylase polypeptide having at least 80%, 85%, 90%, or 95% sequence identity to the wild type glucoamylase polypeptide from Saccharomycopsis fibuligera. Embodiments of glucoamylase polypeptides that can be encoded by the yeast, and also the DNA sequences encoding such peptides that can be integrated in the yeast, are further described in International Patent Application No. PCT/US17/045493, filed 4 Aug. 2017, which is hereby incorporated by reference in its entirety, including all SEQ IDs associated therewith.

In one aspect, the host yeast that is genetically modified is of the species Saccharomyces. In some embodiments, the host yeast is Saccharomyces cerevisiae. In some embodiments, the genetically modified yeast comprises a Saccharomyces cerevisiae yeast, wherein the yeast comprises a heterologous gene encoding a monocarboxylate/proton symporter (e.g., JEN1). In some embodiments, the host yeast is a Saccharomyces cerevisiae yeast that is commercially available for use in ethanol production, such as ETHANOL RED™ yeast, which at the time of this disclosure is available from Lesaffre or a subsidiary thereof.

In one aspect, the yeast is capable of producing ethanol at a fermentation production rate of at least 1.0 g L⁻¹h⁻¹, 2.0 g L⁻¹h⁻¹, 3.0 g L⁻¹h⁻¹, 3.3 g L⁻¹h⁻¹, or 3.75 g L⁻¹h⁻¹. In one aspect, the yeast is capable of producing ethanol at a titer greater than 80 g/L, 90 g/L, 100 g/L, 110 g/L, 120 g/L, 125 g/L 130 g/L, 135 g/L, 140 g/L, 145 g/L, 150 g/L, 155 g/L, 160 g/L, or 165 g/L. In one aspect, the yeast is (a) capable of producing ethanol at a titer of greater than 90 g/L, 100 g/L, 110 g/L, 120 g/L, 130 g/L, or 140 g/L; (b) thermotolerant at temperatures in the range of 33° C. to 40° C., 33° C. to 39° C., 33° C. to 38° C., 33° C. to 37° C., 34° C. to 37° C., 35° C. to 37° C., or 36° C. to 38° C.; or both (a) and (b).

In one aspect, the heterologous gene encoding a monocarboxylic/monocarboxylate transporter is from a yeast of the genus Kluyveromyces. In some embodiments, the heterologous gene encoding a monocarboxylic/monocarboxylate transporter is from Kluyveromyces lactis. In some embodiments, the yeast encodes for a polypeptide having an amino acid sequence with a sequence identity of at least 50%, 55%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, or 99% to any one of the following amino acid sequences: SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 76, or SEQ ID NO: 78. In some embodiments, the yeast comprises one or more of the following residues at the indicated positions in SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, or SEQ ID NO: 62: Lys349, Tyr143, Tyr254, and His373. In one aspect, yeast is used for the production of ethanol or a bioproduct other than ethanol.

In one aspect, the present disclosure relates to fermentation processes using a genetically modified yeast, for example any of the genetically modified yeasts described above. In some embodiments, the process is any process for fermenting a medium to produce ethanol using such genetically modified yeasts. In some embodiments, the process is a continuous fermentation process for manufacturing ethanol comprising: providing a fermentation medium comprising hexose or hexose oligomers, fermenting the fermentation medium with a genetically modified yeast comprising a heterologous monocarboxylate/proton symporter (JEN1) gene, adding one or more feed streams comprising lactate to the fermentation medium, and removing at least one output stream comprising ethanol from the fermentation medium, wherein the average hexose or hexose oligomer concentration of the fermentation medium is at least 5 g/L, the volumetric oxygen uptake rate of the process is at least 0.5 mmol O₂/(L·h), and the process produces ethanol at an overall rate of at least 1.0 g L⁻¹h⁻¹, and the yeast consumes lactate, wherein the at least one output stream contains less than 90% of the lactate added in the one or more feed streams. In some embodiments, the lactate concentration of one or more feed streams has an average lactate concentration of at least 1 g/L. In some embodiments, the feed stream is a vegetable process stream. In some embodiments, the vegetable process stream is a corn process stream or a wheat process stream. In some embodiments, the ethanol titer at the end of the pre-fermenter step is in the range of 20 to 80 g/L. In some embodiments, the lactate consumption rate in the propagator step and/or pre-fermenter step is at least 0.550, 0.600, or 0.650 g L⁻¹h⁻¹. In some embodiments, the ethanol titer of the at least one output stream is at least 90, 100, 110, 120, 130, 140, 150, or 160 g/L.

In some embodiments, the process is a process for manufacturing ethanol comprising: fermenting a medium using a genetically modified yeast comprising a heterologous monocarboxylate/proton symporter (JEN1) gene, wherein the medium comprises glucose or glucose oligomers at a concentration of at least 5 g/L at the start of fermentation, the lactate content of the medium is at least 1 g/L at the start of fermentation, at least 35, 40, 45, 50% or more of the lactate is consumed at the end of fermentation, and the final ethanol titer is at least 90 g/L. In some embodiments, the process has a volumetric oxygen uptake rate (OUR) is at least 0.5, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or 100 mmol O₂/(L·h).

In one aspect, the lactate can be L-lactate, D-lactate, or a mixture thereof. In some embodiments, the pH of the fermentation medium is in the range of about 2 to 7. In some embodiments, the fermentation temperature is in the range of 25 to 45° C., 25 to 40° C., 25 to 35° C., 25 to 30° C., 30 to 45° C., 30 to 40° C., 25 to 38° C., 28 to 38° C., or 30 to 39v° C. In some embodiments, the final ethanol titer of the process is at least 80, 90, 100, 110, 120, 130, 135, 140, 145, 150, 155, or 160 g/liter.

In some embodiments, the dry solids of the fermentation medium is at least 30, 40, 50, 60, 70, or 80 g/L in the fermentation medium. In some embodiments, the dry solids of the fermentation feed is at least 120, 130, 140, or 150 g/L.

In one aspect, the process is a process for manufacturing ethanol comprising: fermenting a medium using a Saccharomyces cerevisiae yeast, for example Ethanol Red™ yeast (commercially available from Lesaffre), wherein the medium comprises glucose or glucose oligomers and lactate, the OUR is at least 0.5, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 mmol O₂/(L·h), the lactate content of the medium is at least 1, 2, 3 or 4 g/L at the start of fermentation, at least 35, 40, 45, or 50% of the lactate is consumed at the end of fermentation, and the final ethanol titer is at least 90 g/L

In one aspect, the method is a method for producing a genetically modified yeast with improved lactate consumption comprising overexpressing one or more heterologous genes encoding a lactate dehydrogenase (cytochrome) (classified as EC 1.1.2.3 or 1.1.2.4) or a heterologous monocarboxylate/proton symporter, and subjecting the yeast to evolution for a characteristic, wherein the yeast is capable of consuming lactate and producing ethanol when the yeast is present in a fermentation medium comprising lactate and glucose. In some embodiments, the characteristic is increased growth rate of the yeast on lactate and/or increased ethanol production of the yeast in the presence of lactate.

In one aspect, in any of the above methods or processes or yeasts, the yeast encodes for a polypeptide having an amino acid sequence with a sequence identity of at least 50%, 55%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, or 99% to any one of the following amino acid sequence: SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 76, or SEQ ID NO: 78. In some embodiments, the yeast comprises one or more of the following residues at the indicated positions in SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, or SEQ ID NO: 62: Lys349, Tyr143, Tyr254, and His373.

In one aspect, in any of the above methods or processes or yeasts, the yeast includes a heterologous nucleic acid regulatory sequence associated with the heterologous gene encoding a monocarboxylic/monocarboxylate transporter. In some embodiments, the heterologous nucleic acid regulatory sequence comprises the ADH1 promoter. In some embodiments, the heterologous nucleic acid regulatory sequence comprises the ADH2 promoter, the PDC1 promoter, or the GPD1 promoter.

In one aspect, the genetically modified yeasts are suitable for ethanol production at a commercially acceptable performance. Accordingly, in any of the above embodiments, the yeast and processes using the yeast are associated with commercially relevant final ethanol titers, ethanol titers at the end of fermentation, or process streams or materials removed from the process having ethanol concentrations of at least 90, 100, 110, 120, 130, 140, 150, or 160 g/L. Further, in some embodiments, any of the above yeasts has a D-, L-, and/or total lactate consumption rate that is greater than a yeast without a heterologous gene encoding a monocarboxylic/monocarboxylate transporter.

In one aspect, any of the genetically modified yeasts comprising a heterologous gene encoding a monocarboxylic/monocarboxylate transporter described above or elsewhere herein are described as capable of consuming lactate and producing ethanol while glucose is present, i.e., while in a fermentation medium comprising glucose. In some embodiments, the fermentation medium comprises a measurable, non-zero concentration of glucose. However, it is contemplated herein that in some embodiments, the glucose concentration of the fermentation medium may not be practically measurable because the glucose may be added to the fermentation medium or otherwise generated within the fermentation medium from glucose oligomers in such a manner that the yeast present in the fermentation medium will consume the glucose immediately. Therefore, it is to be understood that a “fermentation medium comprising glucose” can include a fermentation medium wherein the glucose is not practically measurable due to the glucose being consumed by the yeast as soon as it is generated or added to the fermentation medium.

It is also to be understood that the elements or aspects of any embodiment of the processes, methods, or compositions described above can be applied to any other embodiment, as would be understood by a person skilled in the art.

BRIEF DESCRIPTION OF THE DRAWINGS

The following detailed description of the invention will be better understood when read in conjunction with the appended drawings. It should be understood, however, that the invention is not limited to the precise arrangements and instrumentalities of the embodiments shown in the drawings.

FIG. 1, comprising FIGS. 1A through 1C, is a set of graphs showing glucose consumption, ethanol production, and L-lactate consumption in fermentation shake flask assays for Saccharomyces cerevisiae reference strains (1 and 1-10) and a strain containing an overexpressed CYB2 and JEN1 (1-24).

FIG. 2, comprising FIGS. 2A through 2C, is a set of graphs showing glucose consumption, ethanol production, and D-lactate consumption in fermentation shake flask assays for Saccharomyces cerevisiae reference strains (1 and 1-10) and a strain containing an overexpressed Kluyveromyces lactis JEN1 (1-17).

FIG. 3, comprising FIGS. 3A through 3C, is a set of graphs showing glucose consumption, ethanol production, and D-lactate consumption in fermentation shake flask assays for Saccharomyces cerevisiae reference strains (1 and 1-10), a strain containing an overexpressed K. lactis JEN1 (1-17) and a strain containing an overexpressed K. lactis JEN1 and an overexpressed ScDLD1 (1-30).

FIG. 4, comprising FIGS. 4A and 4B, is a set of graphs showing D,L-lactate consumption and ethanol production in simultaneous saccharification fermentation (SSF) shake flask assays for Saccharomyces cerevisiae reference strains (1 and 1-10) and a strain containing an overexpressed CYB2b and a JEN1 (1-25).

FIG. 5, comprising FIGS. 5A and 5B, is a set of graphs showing D,L-lactate consumption and ethanol production in SSF shake flask assays for Saccharomyces cerevisiae reference strains (1 and 1-10) and a strain containing two copies of both an overexpressed ScCYB2 and a KlJEN1 (1-41).

FIG. 6 is a graph showing L-lactate consumption in shake flask assays for Saccharomyces cerevisiae reference strains (1 and 1-10) and strains containing an overexpressed S. cerevisiae DLD1 and S. cerevisiae CYB2, and selected monocarboxylate/proton symporters.

DETAILED DESCRIPTION

It is to be understood that the figures and descriptions of the present invention provided herein have been simplified to illustrate elements that are relevant for a clear understanding of the present invention, while eliminating other elements found in the related field(s) of art. Those of ordinary skill in the art would recognize that other elements or steps may be desirable or required in implementing the present invention. However, because such elements or steps are well known in the art or do not facilitate a better understanding of the present invention, a discussion of such elements or steps is not provided herein.

Definitions

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one skilled in the art to which this invention belongs. As used herein, each of the following terms has the meaning associated with it as defined in this section.

As used herein, the terms “genetically modified,” “genetically engineered,” and the like refer to the altering of the genetic material of an organism in any way using any genetic engineering technique, including techniques using clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins, i.e., CRISPR/cas systems.

As used herein, “inoculation” is defined as the point in time wherein a microorganism capable of producing a fermentation product is introduced into a fermentation medium.

The terms “bioproduct,” “fermentation product,” and the like are used interchangeably herein and refer to a compound or mixture of compounds produced by an organism via fermentation of a carbon source.

As used herein, “end of fermentation” is defined as the point in time where a fermentation process meets a predetermined endpoint criteria. The predetermined endpoint criteria can include any of the following: a predetermined time interval, exhaustion of the desired fraction of carbon source supplied, cessation of carbon source consumption, or cessation of fermentation product formation. In one embodiment, “end of fermentation” is defined as the point in time where harvesting of the bioproduct is started. As would be understood by a person skilled in the art, “end of fermentation” can refer to a point in time that is different depending on the scale and purpose of the fermentation process. For a large-scale production fermentation process, the “end of fermentation” is preferably the point at which harvesting of the bioproduct is started, i.e., after product formation has effectively stopped. As would be understood by a person skilled in the art, the endpoint criteria for a batch process applies to the entire batch, whereas the endpoint criteria for a continuous process may apply to only a portion of the process, for example a single vessel or unit operation associated with the process, e.g., the process step associated with the pre-fermenter, or may apply to the entire continuous process, i.e., to an output parameter of the continuous process.

As used herein, “cell dry weight” refers to the concentration of dry cell mass present in a fermentation medium at the time of measurement, as measured in a fermentation sample. Cell dry weight is commonly expressed in units of grams/liter (g/L).

As used herein, “cell dry weight at inoculation” refers to the concentration of dry cell mass present in a fermentation medium immediately following inoculation, as measured in a fermentation sample. For fed-batch fermentations, the initial cell dry weight is calculated based on the final volume of fermentation medium. Measurement of dry cell weight is a method known to those skilled in the art. Cell dry weight at inoculation is commonly expressed in units of g/L.

As used herein, “cell dry weight at end of fermentation” refers to the concentration of dry cell mass present in a fermentation medium at the end of fermentation, as measured in a fermentation sample. Cell dry weight at end of fermentation is commonly expressed in units of g/L.

As used herein, “final titer” refers to the concentration of a substance in the fermentation broth at the end of fermentation. The final titer is commonly expressed in units of g/L.

As used herein, “initial titer” refers to the concentration of a substance present at inoculation. The initial titer is commonly expressed in units of g/L.

As used herein, “batch time” refers to the amount of time that has elapsed between the inoculation and the end of fermentation. The batch time is commonly expressed in units of hours (h).

As used herein, “fermentation production rate” for a batch process refers to the final titer minus initial titer of fermentation product (final titer minus initial titer) divided by the batch time. The production rate is commonly expressed in units of grams per liter-hour (g L⁻¹ h⁻¹). When applied to a continuous or semi-continuous process, the “fermentation production rate” is determined using methods known in the art.

As used herein, the “specific production rate” refers to the fermentation production rate divided by the cell dry weight at the end of fermentation. The specific production rate is commonly expressed in units of (g product) (g cells)⁻¹h⁻¹. When applied to a continuous or semi-continuous process, the “specific production rate” is determined using methods known in the art.

As used herein, “product yield” of a fermentation product refers to a ratio of two quantities: a) mass of product (e.g., ethanol) produced in the course of the fermentation (numerator) b) the mass of carbon source added to the fermentation (denominator). The product yield as a percentage is commonly expressed in units of gram per gram (g/g) times 100. Particular note should be taken that product yield is calculated as a ratio of masses. The mass of fermentation product produced should account for the mass of fermentation product present in the fermentation medium at the end of the batch, as well as the mass of any fermentation product harvested during the course of the batch, less the mass of fermentation product present at the start of batch, and further less the mass of any fermentation product added during the course of the batch. The mass of carbon source added to the batch should include the mass of all carbon source(s) present in the fermenter at the start of the batch in addition to the mass of any carbon source(s) added during the course of the batch.

As used herein, “oxygen uptake rate” (“OUR”) refers to the volumetric rate at which oxygen is consumed during a fermentation. Inlet and outlet oxygen concentrations can be measured with exhaust gas analysis, for instance by mass spectrometers. OUR can be calculated by one of ordinary skill in the relevant arts using the Direct Method described in Bioreaction Engineering Principles 2nd Edition, 2003, Kluwer Academic/Plenum Publishers, p. 449, equation 1, which is hereby incorporated by reference. Volumetric OUR is commonly measured in units of (mmol O₂) L⁻¹h⁻¹.

As used herein, “specific oxygen uptake rate” refers to the specific rate at which oxygen is consumed during a fermentation. It is calculated as the ratio of the OUR to the measured cell dry weight. Specific OUR is commonly measured in units of mmol O₂ (g cell dry weight)⁻¹h⁻¹.

The term “exogenous” as used herein with regard to genetic components means that the genetic component is present in a modified version of a microorganism, but is not present in the genome of a native form of the particular microorganism cell. In some embodiments, the exogenous genetic component can be a modified form of a component that was native to the cell, it can be derived from another organism, it can be a modified form of a component derived from another organism, or it can be a synthetically-derived component. For example, the Kluyveromyces lactis JEN1 gene is exogenous when introduced into S. cerevisiae. The term “exogenous” as used herein with regard to a molecule means the molecule originates from outside an organism being referenced, e.g., an enzyme that is exogenous to an organism present in a fermentation broth refers to an enzyme that is not produced and/or secreted by the organism present in the fermentation broth.

As used herein, the term “heterologous” refers to a molecule or activity that is from a source that is different than the referenced organism. In some embodiments, a gene that is referred to as heterologous to a referenced organism is a gene not found in the organism. In some embodiments, an activity that is referred to as heterologous to a referenced organism is an activity not typically associated with that organism. For example, a heterologous activity in a referenced organism can include an overexpression of a gene that is found in the organism. In some embodiments, heterologous can refer to the inclusion of multiple copies of a gene that is found in a referenced organism, i.e., more copies than are typically found in the referenced organism. In some embodiments, a heterologous gene can refer to the inclusion of a gene in a different locus than where the gene is found in the native version of a referenced organism.

Inspection of nucleic acid or amino acid sequences for two nucleic acids or two polypeptides will reveal sequence identity and similarities between the compared sequences. Sequence alignment and generation of sequence identity include global alignments and local alignments which are carried out using computational approaches. An alignment can be performed using BLAST (National Center for Biological Information (NCBI) Basic Local Alignment Search Tool) version 2.2.31 software with default parameters Amino acid % sequence identity between amino acid sequences can be determined using standard protein BLAST with the following default parameters: Max target sequences: 100; Short queries: Automatically adjust parameters for short input sequences; Expect threshold: 10; Word size: 6; Max matches in a query range: 0; Matrix: BLOSUM62; Gap Costs: (Existence: 11, Extension: 1); Compositional adjustments: Conditional compositional score matrix adjustment; Filter: none selected; Mask: none selected. Nucleic acid % sequence identity between nucleic acid sequences can be determined using standard nucleotide BLAST with the following default parameters: Max target sequences: 100; Short queries: Automatically adjust parameters for short input sequences; Expect threshold: 10; Word size: 28; Max matches in a query range: 0; Match/Mismatch Scores: 1, −2; Gap costs: Linear; Filter: Low complexity regions; Mask: Mask for lookup table only. A sequence having an identity score of XX % (for example, 80%) with regard to a reference sequence using the NCBI BLAST version 2.2.31 algorithm with default parameters is considered to be at least XX % identical or, equivalently, have XX % sequence identity to the reference sequence.

As used herein, the terms “lactate,” “lactic acid,” and the like, are used interchangeably unless specifically noted otherwise, and can refer to lactic acid, the conjugate base of lactic acid (lactate), or salts thereof. It is contemplated herein that lactic acid is primarily in the form of the conjugate base when utilized by the organisms described herein, but that the lactic acid or salt forms can also be present and/or utilized by the organisms, as would be understood by a person skilled in the art. Further, “lactate” or “lactic acid” can refer to D-Lactate, L-Lactate, or a mixture thereof. Unless either D- or L-lactate is specifically recited herein, the term “lactate” refers to a mixture of D- and L-enantiomers.

As used herein, the term “hexose” refers to a 6-carbon sugar or a mixture of 6-carbon sugars. In some embodiments, the hexose is glucose or is a mixture of sugars that includes glucose. Throughout this disclosure, any description that refers specifically to glucose alone is also applicable to any hexose or mixture of hexoses.

As used herein, the terms “monocarboxylic transporter,” “monocarboxylate transporter,” “monocarboxylate/proton symporter,” “monocarboxylic acid permease,” “monocarboxylate permease,” “carboxylic acid permease,” and the like are used interchangeably, and refer to transporters that carry monocarboxylate molecules, such as lactate and pyruvate, across cell membranes.

Throughout this disclosure, various aspects of the invention may be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the invention. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 7 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 6, from 2 to 5, from 3 to 5, etc., as well as individual numbers within that range, for example, 1, 2, 3, 3.6, 4, 5, 5.8, 6, 7, and any whole and partial increments in between. This applies regardless of the breadth of the range.

DESCRIPTION

Described herein are genetically modified organisms, methods for producing such organisms, and fermentation processes using such organisms. The organisms can consume lactate during a fermentation process while producing a bioproduct. In one aspect, the organisms can consume lactate in the presence of glucose while producing a bioproduct. Therefore, the present invention relates to organisms and processes that can use lactate as a carbon source for fermentation instead of, or in addition to, carbohydrates. Accordingly, the organisms and processes are useful for fermenting substrates containing lactate, such as corn or other vegetable processing streams.

Many fermentation substrate feed streams, including corn process streams, contain some amount of lactate. For example, the growth of lactate-producing Lactobacilli is often promoted in the steeping step of wet corn milling processes to assist in the breakdown of the corn into its various components. However, most or all of the lactate remains unconsumed in the fermentation broth in currently available fermentation processes. Therefore, the processes and organisms of the present invention can provide a benefit over currently available processes or organisms by consuming a higher percentage of the available carbon sources in the feed stream, resulting in improved fermentation yields, production rates, and/or efficiency.

Genetically Modified Yeasts and Methods for Producing Such Yeasts

In one aspect, the present invention relates to genetically modified yeasts and methods for producing such yeasts. In some embodiments, the genetically modified yeast is of the genus Saccharomyces. In some embodiments, the yeast is a genetically modified Saccharomyces cerevisiae yeast. In one aspect, the yeast is genetically modified to include one or more traits that enable the yeast to consume lactate or improve the lactate consumption capability of the yeast while producing a fermentation product. In some embodiments, the yeast can consume lactate at a faster rate than a yeast without the modification(s) described herein, especially when hexose or hexose oligomers such as glucose are present in the fermentation broth. In some embodiments, the yeast can consume D-lactate, L-lactate, or both D-lactate and L-lactate at a faster rate than a yeast without the modification(s) described herein. In some embodiments, the yeast can produce a bioproduct at a higher titer and/or produce a bioproduct at a faster rate than a yeast without the modification(s) described herein. In some embodiments, the bioproduct is ethanol.

The genetic modifications can include transforming a yeast to contain one or more heterologous genes that relate to lactate consumption or utilization. Non-limiting examples of genetic modifications include: transforming the yeast to overexpress one or more native-type gene(s); transforming the yeast to include multiple copies of one or more native-type gene(s); transforming the yeast with one or more exogenous gene(s); and/or transforming the yeast to include multiple copies of one or more exogenous gene(s).

In one aspect, the genetic modifications can relate to lactate transport, for example transforming a yeast to express a heterologous monocarboxylate/proton symporter gene. In some embodiments, the monocarboxylate/proton symporter gene is from a yeast of the genus Kluyveromyces. In some embodiments, the monocarboxylate/proton symporter gene is a K Lactis (SEQ ID NO: 27), a K. marxianus (SEQ ID NO: 73), or a K. dobzhanskii (SEQ ID NO: 71) JEN1 symporter gene. In some embodiments, the monocarboxylate/proton symporter gene is from a yeast of the genus Yarrowia, for example Yarrowia lypolitica (SEQ ID NO: 79). In some embodiments, the monocarboxylate/proton symporter gene is from a genus of yeast other than genus Kluyveromyces or Yarrowia, for example, but not limited to, Saccharomyces or Issatchenkia. In some embodiments, the monocarboxylate/proton symporter gene is from S. cerevisiae or I. orientalis (SEQ ID NO: 23, SEQ ID NO: 25). In some embodiments, the genetically modified yeast encodes for a polypeptide having an amino acid sequence with a sequence identity of at least 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, or 99% to at least one of the following amino acid sequences: SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 76, or SEQ ID NO: 78. In some embodiments, the yeast encodes for a polypeptide having an amino acid sequence with a sequence identity of at least 70%, 74% or 75% to either the K Lactis (SEQ ID NO: 28) or K. dobzhanskii (SEQ ID NO: 76) JEN1 polypeptides, or both.

In some embodiments, the genetic modifications can relate to lactate consumption or utilization. In some embodiments, the yeast is transformed to express one or more heterologous genes encoding a lactate dehydrogenase (cytochrome) (EC 1.1.2.3 or 1.1.2.4). In some embodiments, the yeast is transformed to express a heterologous cytochrome b2 (CYB2) gene. In some embodiments, the CYB2 gene is a S. cerevisiae (SEQ ID NO: 13) or I. orientalis CYB2 (SEQ ID NO: 16) gene. In some embodiments, the CYB2 gene is from S. kluyveri (SEQ ID NO: 53), S. bayanus (SEQ ID NO: 55), Z. rouxii (SEQ ID NO: 57), K. lactis (SEQ ID NO: 59), or K. dobzhanskii (SEQ ID NO: 61). In some embodiments, the genetically modified yeast having a heterologous CYB2 gene encodes for a polypeptide having an amino acid sequence with a sequence identity of at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, or 99% to at least one of the following amino acid sequences: SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, or SEQ ID NO: 62.

In some embodiments, the yeast is transformed to express a heterologous D-lactate dehydrogenase (DLD) gene. In some embodiments, the DLD gene is a S. cerevisiae (SEQ ID NO: 39) or I. orientalis DLD (SEQ ID NO: 41) gene. In some embodiments, the DLD gene is from S. kluyveri (SEQ ID NO: 63), S. bayanus (SEQ ID NO: 65), A. fumigatus (SEQ ID NO: 67), K. lactis (SEQ ID NO: 69), K. dobzhanskii (SEQ ID NO: 71), or K. marxianus (SEQ ID NO: 73). In some embodiments, the genetically modified yeast having a heterologous DLD gene encodes for a polypeptide having an amino acid sequence with a sequence identity of at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, or 99% to at least one of the following amino acid sequences: SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO:64, SEQ ID NO: 66, SEQ ID NO:68, SEQ ID NO: 70, SEQ ID NO: 72, or SEQ ID NO: 74. In some embodiments, the yeast is transformed to express both a heterologous CYB2 gene and a DLD gene.

In one aspect, the genetically modified yeast can be transformed to include any combination of heterologous monocarboxylate/proton symporter genes and lactate dehydrogenase genes. In some embodiments, the yeast contains a heterologous monocarboxylate/proton symporter gene, a heterologous CYB2 gene, and a heterologous DLD gene. In some embodiments, the yeast contains a heterologous monocarboxylate/proton symporter gene and a heterologous CYB2 gene. In some embodiments, the yeast contains a heterologous monocarboxylate/proton symporter gene and a heterologous DLD gene. In some embodiments, the yeast contains more than one copy of any of a heterologous monocarboxylate/proton symporter gene, a heterologous CYB2 gene, and/or a heterologous DLD gene, i.e., the yeast can be transformed with two or more copies of a heterologous monocarboxylate/proton symporter gene; two or more copies of a heterologous CYB2 gene; and/or two or more copies of a heterologous DLD gene. Further, the yeast can be modified to contain heterologous genes from any combination of species, for example, a S. cerevisiae yeast can be modified to contain one or more copies of a K. lactis JEN1, one or more copies of a heterologous S. cerevisiae CYB2, and one or more copies of a heterologous S. cerevisiae DLD. Accordingly, the yeast can encode for a polypeptide having an amino acid sequence with a sequence identity of at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, or 99% to one, two, three, or more of a monocarboxylate/proton symporter-related, CYB2-related, and/or DLD-related amino acid sequence, for example at least one of SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 76, SEQ ID NO: 78, SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO: 62, SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO:64, SEQ ID NO: 66, SEQ ID NO:68, SEQ ID NO: 70, SEQ ID NO: 72, or SEQ ID NO: 74.

While not wishing to be bound by theory, it is contemplated herein that the lactate consumed by the organism is converted primarily to pyruvate, and at least a portion of the pyruvate is converted to the desired fermentation product. Even lactate that is consumed by the organism for respiration can provide a benefit because the organism is using lactate instead of other potentially preferred carbon sources such as glucose.

Strains of Saccharomyces cerevisiae that can consume D-lactate and produce ethanol have been described (Wakamatsu et al., 2013, Biosci. Biotechnol. Biochem. 77(5) 1114-1116). However, the strains described in Wakamatsu produced ethanol from a fermentation medium containing only lactate, and not from a medium that also contains glucose. Further, Andrade described that JEN1 expression is inhibited by the presence of glucose (Andrade et al., 2001, Fungal Genetics and Biology 32, 105-111). Therefore, currently available yeast strains cannot consume significant amounts of lactate and glucose simultaneously while producing a fermentation product at a commercially useful rate. Further, it is known that many yeasts produce some lactic acid rather than consuming lactic acid during fermentation. However, the present invention relates to genetically modified yeasts that can surprisingly use both lactate and glucose as a carbon source simultaneously to produce a fermentation product at rates suitable for commercial applications. In one aspect, the genetically modified yeast can consume L-lactate at significantly higher rates than currently available yeast, whether or not glucose or another hexose is present.

In one aspect, the yeast can be genetically modified to consume D-lactate, L-lactate, or a mixture of D- and L-lactate. Vegetable processing streams that contain lactate typically contain a mixture of D-lactate and L-lactate enantiomers, for example a racemic mixture or a mixture containing some ratio of D- and L-lactate other than 50:50. In one aspect, the yeast can be genetically modified to contain a heterologous lactate racemase-expressing gene. A yeast that contains a racemase expressing gene can be used to improve the lactate-consuming characteristics of the yeast. For example, a genetically modified yeast according to the present invention that can consume D-lactate more quickly than L-lactate can be modified to express a lactate racemase. As the D-lactate is consumed more quickly by the yeast, the racemase can be used to convert L-lactate to D-lactate to improve the overall rate of lactate consumption.

As described above, the yeast can include heterologous JEN1, DLD, and/or CYB2 gene(s), resulting in encoding polypeptides having a minimum sequence identity to certain amino acid sequences listed herein. In some embodiments, signature patterns at positions corresponding to specific residue ranges have been identified. In some embodiments, the yeast of the present invention is transformed with a construct having these patterns conserved. Accordingly, in some embodiments, the yeast can encode for polypeptides having a signature pattern at certain amino acid residue positions.

In one aspect, the genetically modified yeast encodes for a CYB2 protein having the following amino acid residues conserved at the specified positions: Lys349, Tyr143, Tyr254 and His373. Xia describes the involvement of these residues in the catalytic oxidation of lactate to pyruvate (Xia and Mathews, 1990, J. of Molecular Biology. 212 pp. 837-863, which is hereby incorporated by reference in its entirety). In some embodiments, the yeast of the present invention encodes a polypeptide having a sequence identity of at least 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95% to SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, or SEQ ID NO: 62, that includes one or more of the following amino acid residues at the indicated positions: Lys349, Tyr143, Tyr254 and His373. The amino acids Lys349, Tyr143, Tyr254 and His373 have a role in the mechanism of lactate oxidation via interaction with pyruvate. In some embodiments, such a yeast includes a heterologous CYB2 gene from any of the following species: S. bayanus, S. kluyveri, Zygosaccharomyces rouxii, K. lactis, K. dobzhanskii, K. marxianus, L. orientalis, Aspergillus fumigatus, or A. niger. In some embodiments, such a yeast also includes at least one heterologous monocarboxylate/proton symporter gene and encodes for a polypeptide having a sequence identity of at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% to SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 76, or SEQ ID NO: 78. In some embodiments, such a yeast also includes at least one heterologous DLD gene and encodes for a polypeptide having a sequence identity of at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% to SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 72, or SEQ ID NO: 74.

In one aspect, the genetically modified yeast can consume D-lactate, L-lactate, or a mixture thereof at a faster rate than currently available yeasts. In some embodiments, the genetically modified yeast can consume D-lactate and/or L-lactate, in conditions where currently available yeasts cannot consume D-lactate and/or L-lactate. In one aspect, it is useful to measure the lactate consumption rate according to the Evaluation Protocol for Lactate Consumption described later herein. In some embodiments, the yeast has a L-lactate consumption rate of at least 0.030 gL⁻¹h⁻¹ when the concentration of hexose is 150 g/L or greater. In some embodiments, the yeast has a L-lactate consumption rate of at least 0.035, 0.040, 0.045, or 0.050 gL⁻¹h⁻¹ when the concentration of hexose is 150 g/L or greater. In some embodiments, the yeast has a L-lactate consumption rate of at least 0.015, 0.020, 0.025, 0.030, 0.035, or 0.040 gL⁻¹h⁻¹ when the concentration of hexose is 5 g/L or greater. In some embodiments, the yeast has a D-lactate consumption rate of at least 0.005, 0.006, 0.007, 0.008, 0.009, 0.010, 0.015, 0.020, 0.025, or 0.030 gL⁻¹h⁻¹ when the concentration of hexose is 150 g/L or greater. In some embodiments, the yeast has a D-lactate consumption rate of at least 0.015, 0.020, 0.025, 0.030, 0.035, or 0.040 gL⁻¹h⁻¹ when the concentration of hexose is 5 g/L or greater.

In some embodiments, the yeast can include other genetic modifications. In one aspect, the yeast can be transformed to express enzymes useful for improving the production of a bioproduct. In one aspect, the yeast can be transformed to contain genes related to expressing enzymes that are typically added to a fermentation process, for example, enzymes used to generate glucose or another hexose from hexose oligomers. In one aspect, the yeast can be transformed to reduce or eliminate the conversion of the carbon source(s) to undesired compounds. In some embodiments, the yeast can include one or more genetic modifications useful for improving any other aspects of an ethanol production process. Non-limiting examples of genetic modifications that can useful for an ethanol-producing yeast include transforming the yeast to express a heterologous gene for producing glucoamylase (EC 3.2.1.3), for example the yeast expresses a glucoamylase from Saccharomycopsis fibuligera or Rhizopus oryzae; transforming the yeast to express a heterologous gene for consuming isomaltose; and/or transforming the yeast to reduce the formation of glycerol in the yeast during fermentation. In some embodiments, the yeast can be transformed to secrete a heterologous lactate oxidase. Further, the yeast can be transformed to secrete heterologous catalase in addition to the lactate oxidase to consume hydrogen peroxide.

In some embodiments, the genetic modifications to the yeast associated with increasing the consumption of lactate (e.g., a yeast modified to include a heterologous CYB2 gene, DLD gene, and/or JEN1 gene) can also relate to the reduction of glycerol produced by the yeast during fermentation. The reduction of glycerol produced during fermentation can increase the amount of carbon transformed from the carbon source(s) (e.g., glucose and/or lactate) into the fermentation product. Accordingly, the yeast can produce a higher yield of a fermentation product, such as ethanol, and generate a lower amount of glycerol than a yeast that does not include the genetic modifications associated with increased lactate consumption.

In some embodiments, the yeast can be further engineered by a method other than genetic modification. In some embodiments, after the yeast is genetically modified as described above, the yeast is evolved. In some such embodiments, the evolution can include propagating the yeast for multiple generations to allow for the yeast to naturally select for certain characteristics.

In some embodiments, the yeast can be modified by mutagenesis. In some such embodiments, the yeast can be selected for certain characteristics after mutagenesis. In some embodiments, the mutagenesis can include subjecting the yeast to ultraviolet radiation and/or chemical treatment. In some embodiments, the selected characteristics of the yeast can include heat tolerance, ethanol tolerance, inhibitor tolerance, improved growth rate, and/or by-product reduction.

Accordingly, in one aspect, the present invention also relates to a method for evolving a yeast that can consume lactate while producing a fermentation product. In some embodiments, the method includes the steps of: transforming a yeast to express one or more heterologous genes associated with increased lactate consumption, then evolving the yeast and selecting the yeast based on a desired characteristic. In some embodiments, the method includes the steps of: transforming a yeast to express one or more heterologous genes associated with increased lactate consumption, exposing the yeast to an environment capable of causing mutagenesis, and selecting the yeast for one or more desired characteristics. In one aspect, the method for evolving the yeast can use any yeast described herein, i.e., a genetically modified yeast transformed to increase lactate consumption during fermentation.

In one aspect, the non-natural yeast of the present invention has the ability to grow, and/or can produce a fermentation product at temperatures that are greater than those in which yeast, for example Saccharomyces cerevisiae, typically are used in fermentation processes. For example, S. cerevisiae typically have optimal growth at a temperature of about 30° C. In some embodiments, the yeast has a greater tolerance to elevated temperatures, such as 32° C. or greater, such as in the range of greater than 32° C. to about 40° C. Exemplary ranges for elevated temperature are Tito T2, wherein T₁ is selected from 32.2° C., 32.4° C., 32.6° C., 32.8° C., 33° C., 33.2° C., 33.3° C., 33.4° C., 33.6° C., 33.8° C., 34° C., 34.2° C., 34.4° C., 34.6° C., 34.8° C., 35° C., and 36° C.; and T2 is selected from 36° C., 37° C., 38° C., 39° C., and 40° C. For the purposes of this disclosure, a yeast is considered “thermotolerant” if the yeast can continue to grow, reproduce, and/or produce a fermentation product during or after being exposed to a fermentation medium having an elevated temperature.

During a fermentation process the fermentation medium can reach an elevated temperature of 32° C. or greater during one or more time(s) during the fermentation process. The temperature can be elevated during part of the fermentation period, or during the entire fermentation period. The temperature can be elevated for 5 minutes of greater, 10 minutes of greater, 30 minutes or greater, 1 hour or greater, 2 hours or greater, 5 hours or greater, or 10 hours or greater. The time of elevated temperature can also be expressed as a total of the overall fermentation period, such as about 0.1% to 100%, about 0.1% to about 75%, about 0.1% to about 50%, about 0.1% to about 25%, about 0.1% to about 10%, about 0.1% to about 5%, about 0.1% to about 2.5%, about 0.1% to about 1%, or about 0.1% to about 0.5% of the fermentation period.

The engineered yeast can also provide a commercially relevant titer of ethanol during or after the period of elevated temperature. For example, during or after the period of elevated temperature, for example, any of the ranges corresponding to T₁ to T₂, the ethanol titer can be in the range of about 110 g/L to about 170 g/L, in the range of about 125 g/L to about 170 g/L, or in the range of about 140 g/L to about 170 g/L. Accordingly, the engineered yeast described herein can produce ethanol at a commercially useful titer during or after a period of high temperature that would typically cause issues in other currently available yeast strains used in ethanol-producing fermentation processes. Such issues include but are not limited to: death to a significant percentage of yeast cells; deleterious effects on the ability of the yeast to reproduce; and/or reduction or elimination of the ability of the yeast to produce a fermentation product.

An engineered S. cerevisiae described herein can be put under temperature selection pressure to select for strains that demonstrate increased tolerance to growth at higher temperatures. The engineered yeast can be subjected to random mutagenesis (e.g., UV, chemical) prior to application of the higher temperature selection to generate mutation(s) that can confer improved tolerance to growth at these higher temperatures. For example, an engineered yeast of the disclosure can have a specific growth rate at a temperature in the range of 32° C. or greater that that is 10%, 20%, 30%, 40%, or 50% greater than the growth rate of a reference yeast. In some embodiments, the reference yeast is a yeast expressing a Saccharomycopsis fibuligera glucoamylase that is capable of producing ethanol at a titer of at least 90 g/L. In one aspect, this disclosure also relates to a method for producing a yeast product suitable for use in a fermentation process. In some embodiments, such a method includes the steps of growing a yeast, for example any of the engineered yeasts described herein, and isolating the yeast from the medium used to grow the yeast. The method can further include the step of drying the yeast to form a yeast product. Drying the yeast can improve the shelf-life of the yeast. In some embodiments, the dried yeast has a moisture content of less than 5%, less than 4%, less than 3%, less than 2%, or less than 1%.

Fermentation Processes

In one aspect, the present invention relates to fermentation processes. In one aspect, the fermentation processes can be any process using an embodiment of the genetically modified yeasts described herein to produce a fermentation product. In some embodiments, the fermentation product is ethanol. In some embodiments, the fermentation product can be an alcohol other than ethanol, for example, but not limited to, n-propanol, iso-propanol, n-butanol, iso-butanol, butadiene, or isoprene.

An exemplary fermentation process can include the steps of providing a fermentation medium that contains a carbon source, adding a yeast to the fermentation medium, fermenting the medium with the yeast to produce a bioproduct, and harvesting the bioproduct. In one aspect, the carbon source in the medium can include starches, sugars, organic acids, or a mixture thereof. In some embodiments, the carbon source in the medium is a mixture of glucose oligomers, glucose, and/or lactate.

In one aspect, a lactate-containing vegetable process stream is used as the fermentation medium or is added to the fermentation medium at some point in the fermentation process. In one aspect, the processes of the present invention can be used to ferment a fermentation medium containing a significant amount of lactate in addition to glucose and/or glucose oligomers. Non-limiting examples of fermentation media containing a significant amount of lactate include media having at least 0.1, at least 0.5, at least 1, at least 2, at least 3, at least 4, or at least 5 g/L lactate. In some embodiments, the fermentation media can have a lactate content in the range of about 1-20, 2-20, 3-20, 4-20, 5-20, 1-15, 3-15, or 5-15 g/L at the start of fermentation. In some embodiments, the fermentation media can have a lactate content in the range of about 1-50, 15-30, or 20-30 g/L at the start of fermentation. For example, in some embodiments, light steep water (LSW) can contain about 25 g/L lactate.

In some embodiments, the processes described herein can be used to consume most or all of the lactate in the fermentation medium. In some embodiments, the processes can be used to consume only a portion of the lactate in the fermentation medium. The consumption of lactate during the process can depend on a number of factors, including, but not limited to: the characteristics of the yeast used; the rate of oxygen added to the process; the amount of oxygen present at the start of fermentation; the glucose concentration in the fermentation medium, pH, and temperature.

In one aspect, as would be understood by a person skilled in the art, the composition of the medium can vary during fermentation. For example, glucose or another hexose can be generated from oligomers during fermentation via enzymatic activity, then consumed. Accordingly, in some embodiments, the glucose content can be very low or even undetectable at some points of the fermentation if glucose is consumed by the yeast faster than it is generated from the glucose oligomers. In some embodiments, for example fed-batch fermentation, the medium can be continuously or semi-continuously supplemented with a feed stream, such as a vegetable process feed stream. In some embodiments, the lactate content can be very low or even undetectable at some points of the fermentation due to consumption by the yeast, and then more lactate can be added to the medium via a vegetable process feed stream.

Accordingly, in one aspect, the concentrations of various components of the fermentation medium for the processes described herein can be an average concentration. Average concentrations of components can be calculated via known methods in the art, for example by taking the average of the concentration of a component in the fermentation medium at the start of fermentation and the concentration of the same component in the fermentation medium of the end of fermentation. Such a calculation of average can also account for the concentration of the component in any input and/or output streams during the fermentation process. Further, for a continuous fermentation process, the average concentration of a component can refer to the average concentration in any single vessel, or it can refer to the average concentration over the entire process, i.e., accounting for all feed streams and all output streams of the process.

In some embodiments, at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 99% of the lactate present in the fermentation medium and/or added to the fermentation medium is consumed by the end of fermentation. In some embodiments, the rate of lactate consumption during fermentation is in the range of 0.01 to 1.5 g L⁻¹h⁻¹, 0.05 to 1 g L⁻¹h⁻¹, or 0.1 to 1 g L⁻¹h⁻¹. In some embodiments, the rate of lactate consumption during fermentation is at least 0.01 g L⁻¹h⁻¹, 0.05 g L⁻¹h⁻¹, 0.1 g L⁻¹h⁻¹, 0.5 g L⁻¹h⁻¹, or 1 g L⁻¹h⁻¹. In some embodiments, the rates of lactate consumption listed above can refer to the average lactate consumption during fermentation. In some embodiments, the rates of lactate consumption listed above can refer to the lactate consumption during the first portion of the fermentation process, for example, over the first 10 hours, 8 hours, 6 hours, 4 hours, 2 hours, 1 hours, or 30 min of the fermentation process. In some embodiments, the rates of lactate consumption listed above refer to the rate of lactate consumption when glucose is present. In some embodiments, the glucose concentration is at least 0.1 g/L, 1 g/L, 10 g/L, 20 g/L, or 30 g/L when the rate of lactate consumption during fermentation is at least 0.01 g L⁻¹h⁻¹, 0.05 g L⁻¹h⁻¹, 0.1 g L⁻¹h⁻¹, 0.5 g L⁻¹h⁻¹, or 1 g L⁻¹h⁻¹.

In some embodiments, the amount of total lactate in the fermentation medium at the end of fermentation is in the range of 0 to 3 g/L, 0 to 1 g/L, 0 to 0.5 g/L, 0 to 0.1 g/L, 0.001 to 3 g/L, 0.001 to 1 g/L or 0.001 to 0.1 g/L. In some embodiments, the amount of total lactate in the fermentation medium at the end of fermentation is less than 3 g/L, 2 g/L, 1 g/L, 0.5 g/L, or 0.1 g/L. In some embodiments, the amount of L-lactate in the fermentation medium at the end of fermentation is in the range of 0 to 3 g/L, 0 to 1 g/L, 0 to 0.5 g/L, 0 to 0.1 g/L, 0.001 to 1 g/L or 0.001 to 0.1 g/L. In some embodiments, the amount of L-lactate in the fermentation medium at the end of fermentation is less than 3 g/L, 2 g/L, 1 g/L, 0.5 g/L, or 0.1 g/L. In some embodiments, the amount of D-lactate in the fermentation medium at the end of fermentation is in the range of 0 to 3 g/L, 0 to 1 g/L, 0 to 0.5 g/L, 0 to 0.1 g/L, 0.001 to 1 g/L or 0.001 to 0.1 g/L. In some embodiments, the amount of D-lactate in the fermentation medium at the end of fermentation is less than 3 g/L, 2 g/L, 1 g/L, 0.5 g/L, or 0.1 g/L.

In one aspect, the process of the present invention can be used to produce ethanol at commercially significant rates and/or titers. In some embodiments, the rate of ethanol produced can be 1 to 6 g L⁻¹h⁻¹, 1 to 5.5 g L⁻¹h⁻¹, or 1 to 5 g L⁻¹h⁻¹. In some embodiments, the ethanol titer at the end of fermentation is at least 90 g/L, 100 g/L, 110 g/L, 120 g/L, 125 g/L, 130 g/L, 131 g/L, 132 g/L, 133 g/L, 134 g/L, or at least 135 g/L. In some embodiments, the ethanol titer at the end of fermentation is in the range of 120 g/L to 155 g/L, 130 to 155 g/L, 135 to 155 g/L, 130 to 150 g/L, or 130 to 140 g/L.

In one aspect, the process can use a yeast other than the genetically-modified yeasts described herein, for example the commercially available ETHANOL RED™ yeast (available from Lesaffre/Fermentis), and the process can be run using a high oxygen uptake rate and/or a lower glucose concentration to promote lactate consumption.

In one aspect, the process can be used to consume L-lactate, D-lactate, or a mixture of L- and D-lactate. In one aspect, the process can include using a lactate racemase to improve the lactate-consuming characteristics of the yeast. In some embodiments, the yeast used in the process can be a genetically-modified yeast that secretes a lactate racemase. In some embodiments, the exogenous lactate racemase can be added to process instead of, or in addition to, lactate racemase secreted by the yeast. Other exogenous enzymes can be added to the process. For example, in some embodiments an exogenous lactate oxidase can be added to the process. In one such embodiment, exogenous catalase can be added to the process to decompose hydrogen peroxide formed by the activity of the exogenous lactate oxidase.

Batch Fermentation Processes

In one aspect, the process of the present invention can be a batch fermentation process. In some embodiments, the batch process of the present invention is a dry-grind or dry-milling ethanol production process. Batch fermentation processes, including dry-grind ethanol processes are well-known in the art. As would be understood by a person skilled in the art, lactate can be formed during the dry milling of corn or other vegetable matter, for example, as a result of bacterial contamination. In one aspect, the genetically modified yeast of the present invention can be used in a batch fermentation process to produce a fermentation product using lactate as a carbon source.

An exemplary batch fermentation process includes the steps of providing a fermentation medium that contains lactate and/or other carbon sources such as carbohydrates and fermenting the medium using a genetically modified yeast of a type described herein. In some embodiments, the yeast contains a heterologous monocarboxylate/proton symporter (e.g., JEN1) gene. In some embodiments, the medium contains glucose or glucose oligomers at concentration of at least 0.5, 1, 2, or 3 g/L at the start of fermentation. In some embodiments, the lactate concentration is at least 0.5, 1, 2, 3, 4, 5, or 6 g/L at the start of fermentation. In some embodiments, the lactate concentration is in the range of 1 to 20 g/L, 1 to 15 g/L, 1 to 10 g/L, 1 to 8 g/L, or 1 to 5 g/L at the start of fermentation. In some embodiments, at least 20, 30, 40, 50, 60, 70, 80, 90, 95, or 99% of the total lactate is consumed at the end of fermentation. In some embodiments, at least 50, 60, 70, 80, 90, 95, or 99% of the D-lactate is consumed at the end of fermentation. In some embodiments, at least 50, 60, 70, 80, 90, 95, or 99% of the L-lactate is consumed at the end of fermentation.

In one aspect, the batch fermentation process is run with a minimum volumetric oxygen uptake rate (OUR) for at least a part of the process. In some embodiments, the OUR is at least 0.5, 1.0, or 1.5 mmol O₂/(L·h) during at least part of the process. In some embodiments, the OUR is in the range of 0.5 to 5.0 mmol O₂/(L·h) during at least part of the process. In some embodiments, the OUR is in the range of 3.5 to 4.5 mmol O₂/(L·h) during at least part of the process. In some embodiments, the OUR is at least 0.5, 1.0, or 1.5 mmol O₂/(L·h) for the initial part of the process. In some embodiments, the OUR is at least about 0.5 or 1.0, or 1.5 mmol O₂/(L·h) for the first 6, 8, or 10 hours of the process. In some embodiments, the OUR is reduced or about zero during part of the process. In some embodiments, the OUR is less than 0.5 or 1.0 mmol O₂/(L·h) after about the first 6, 8, 10, 12, 15, or 20 hours of the process.

Continuous Fermentation Processes

In one aspect, the process of the present invention can be a continuous or a semi-continuous fermentation process. In some embodiments, the continuous process of the present invention is a wet corn milling ethanol production process. Continuous fermentation processes, including wet milling ethanol processes are well-known in the art. In some embodiments, a fermentation process having a continuous mode of operation includes multiple fermenters that operate in series in which a starch hydrolysate is supplied in the first fermenter, which is fed to second fermenter and so on until the starch hydrolysate is converted to ethanol. In some embodiments, continuous operation can be operated using between 1 to 10 or 2 to 7 fermenters. In some embodiments, a continuous fermentation process can be performed in a single vessel, in which feedstock can be added and product-containing broth can be removed on a continuous or semi-continuous schedule.

An exemplary continuous fermentation process for manufacturing ethanol comprises the following steps: providing an initial fermentation medium that contains glucose or glucose oligomers, fermenting the fermentation medium with a genetically modified yeast, adding one or more feed streams comprising lactate to the fermentation medium, and removing at least one output stream comprising ethanol from the fermentation medium. In some embodiments, the initial fermentation medium can contain lactate and/or other carbon sources in addition to glucose or glucose oligomers. In one aspect, the genetically modified yeast is a yeast according to any of the embodiments of a genetically modified yeast described herein. In some embodiments, the yeast contains a heterologous monocarboxylate/proton symporter (e.g., JEN1) gene.

In some embodiments, the initial fermentation medium is added to a pre-fermenter or growth fermenter vessel, where the genetically modified yeast is added and grown until a desired biomass is achieved. In some embodiments, the conditions of the process in the pre-fermenter are set to favor cell growth over fermentation product formation. In some embodiments, the contents of the pre-fermenter vessel can then be transferred to a second fermenter vessel. In the second fermenter vessel, the conditions of the process are set to favor the formation of fermentation product over cell growth. In some embodiments, additional fermentation medium is added to the second fermenter vessel, either in a single portion or in a continuous or semi-continuous manner. In some embodiments, the additional fermentation medium added to the second fermenter vessel contains lactate and/or other carbon sources. The second fermenter referred to above can also be referred to as a “propagator.” In some embodiments, the contents of the second fermenter vessel can be transferred to a third fermenter vessel. The process conditions of the third fermenter vessel can be the same or different as the second fermenter vessel. In some embodiments, the contents of third fermenter vessel can be transferred to one or more additional fermenter vessels, as would be understood by a person skilled in the art of continuous fermentation processes. In some embodiments, the bioproduct, e.g., ethanol, is isolated from the contents of the final fermenter vessel.

In some embodiments, the average glucose concentration of the fermentation medium in the pre-fermenter vessel is in the range of 10 to 20 g/L. In some embodiments, the average glucose concentration of the fermentation medium in the second fermenter vessel is in the range of 30 to 40 g/L. In some embodiments, the average glucose concentration of the fermentation medium in the third fermenter vessel, or any additional fermenter vessel, is in the range of 30 to 40 g/L. In some embodiments, the average glucose concentration of the fermentation medium in the final fermenter vessel is in the range of 0 to 5 g/L. In some embodiments, the average glucose concentration of the fermentation medium in the pre-fermenter vessel, propagator vessel, or in any of the fermentation vessels is in the range of 0-5, 2-5, 1-10, 5-10, 5-15, 5-20, 10-20, 15-25, 20-30, 25-35, 30-40, or 35-45 g/L. In some embodiments, the average glucose concentration of the fermentation in the pre-fermenter vessel, propagator vessel, or in any of the fermentation vessels is maintained in a range that is greater than or equal to the glucose concentration associated with glucose repression in a yeast. In some embodiments, the glucose concentration associated with glucose repression in a yeast is in the range of 2 to 5 g/L. Accordingly, in such embodiments, the average glucose concentration of the fermentation medium in the pre-fermenter vessel or in any of the fermentation vessels can be maintained at a level greater than or equal to 2, 3, 4, or 5 g/L.

Other fermentation conditions can be adjusted and/or maintained in the continuous fermentation process, including, but not limited to: temperature, pH, volumetric or specific oxygen uptake rate (OUR), or the concentration of any carbon source or any fermentation medium nutrient. In some embodiments, the temperature in the pre-fermenter vessel, propagator vessel, or in any other fermentation vessel can be in the range of 20-45, 20-40, 20-30, 25-35, or 30-40° C. In some embodiments, the pH in the pre-fermenter vessel, propagator vessel, or in any other fermentation vessel can be in the range of 2 to 7, 3 to 6, 4.5 to 5.5, or 3.5 to 4.5. As would be understood by a person skilled in the art, the pH at the start of fermentation can be lower than the pH at the end of fermentation as a result of lactate being consumed by the yeast. Accordingly, the pH at the end of fermentation can be in a different range of those listed above than the pH at the start of fermentation. In some embodiments, the volumetric OUR in the pre-fermenter vessel, propagator vessel, or in any other fermentation vessel is at least 0.5 mmol O₂/(L·h) or at least 1 mmol O₂/(L·h). In some embodiments, the volumetric OUR in the pre-fermenter vessel, propagator vessel, or in any other fermentation vessel is in the range of 0.1 to 5 mmol O₂/(L·h), 3 to 5 mmol O₂/(L·h), 0.2 to 1 mmol O₂/(L·h), 0.4 to 0.6 mmol O₂/(L·h), 4 to 200 mmol O₂/(L·h), 8 to 10 mmol O₂/(L·h), or 4 to 30 mmol O₂/(L·h). In some embodiments, the volumetric OUR in the pre-fermenter vessel, propagator vessel, or in any other fermentation vessel is at least 4 mmol O₂/(L·h), at least 5 mmol O₂/(L·h), at least 6 mmol O₂/(L·h), at least 7 mmol O₂/(L·h), or at least 8 mmol O₂/(L·h).

In some embodiments, the cell density in the pre-fermenter vessel is in the range of 3 to 10 g/L or 5 to 10 g/L. In some embodiments, the cell density in the propagator vessel is in the range of 10 to 50 g/L

In one aspect, as described herein, the yeast consumes lactate during the fermentation process. In some embodiments, the total lactate content in the sum of all output streams is less than 90% of the lactate added to the fermentation process, i.e., the lactate content in sum of all input or feed streams. In some embodiments, the total lactate content in the output of the fermentation process is less than 99%, 95%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15%, or 10% of the input to the fermentation process. In some embodiments, the total D-lactate content in the output of the fermentation process is less than 99%, 95%, 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15%, or 10% of the input to the fermentation process. In some embodiments, the total L-lactate content in the output of the fermentation process is less than 99%, 95%, 90%, 85%, 80%, 75%, 70%, 65%, 60%, 55%, 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15%, or 10% of the input to the fermentation process.

The continuous fermentation processes described herein can produce ethanol or another bioproduct at commercially significant rates. In some embodiments, the processes can produce the bioproduct at a rate of at least 0.5, 1.0, 1.5, 2.0, 2.5, 3.0, or 3.2 g

Advantages in Producing Certain Bioproducts

In one aspect, the lactate-consuming characteristics of the yeast can provide advantages in producing certain bioproducts, or in certain fermentation processes. The genetically modified yeasts and fermentation processes described herein can be used to make ethanol or other bioproducts of interest. Other bioproducts, include alcohols other than ethanol, lactic acid, 3-hydroxypropionic acid (3-HP), and succinic acid.

In some embodiments, the yeasts described herein can be useful for making enantiomerically-pure lactic acid. For example, by consuming one enantiomer with relatively high specificity, the yeast can produce D-lactic acid or L-lactic acid having enantiomeric purities of greater than 95%, 97%, 98%, 99%, 99.5% or more.

In some embodiments, the yeasts can improve the production of organic acids such as succinic acid or 3-HP. For example, it can be problematic to separate lactic acid from an organic acid product when recovering the organic acid product from the fermentation broth in downstream processing. By consuming lactate, the yeasts described herein can improve the efficiency of downstream processing and/or improve the purity of the final organic acid product.

In one aspect, the yeasts described herein can enable the use of vegetable process streams in fermentation processes that cannot typically use such streams. Vegetable process streams, such as corn steep liquor, are not typically used to produce bioproducts other than ethanol due to impurities such as lactate present in these streams. By consuming the lactate, the yeasts of the present invention can enable vegetable process streams to be used in a wide variety of fermentation processes.

EXPERIMENTAL EXAMPLES

The invention is further described in detail by reference to the following experimental examples. These examples are provided for purposes of illustration only, and are not intended to be limiting unless otherwise specified. Thus, the invention should in no way be construed as being limited to the following examples, but rather should be construed to encompass any and all variations which become evident as a result of the teaching provided herein.

Evaluation Protocol for Lactate Consumption

The protocol described below is used to determine the consumption of L-lactate, D-lactate, or a mixture of D- and L-lactate (i.e., “total lactate”) by a yeast strain.

A yeast strain is selected and streaked out on a ScD-Ura plate and incubated at 30° C. until single colonies are visible (1-2 days) or grown overnight in 4 ml of YP+100 g/L D-glucose in a 14 ml culture tube as a liquid culture at 30° C./250 rpm to generate seed biomass. A shake flask is inoculated with seed cell slurry to reach an initial OD₆₀₀ of 0.1-0.3. Immediately prior to inoculating, 60 mL of shake flask medium is added to a 250 mL non-baffled shake flask (Corning 4995-250) fitted with a screw cap containing a gas-permeable seal (corning 1395-45LTMC). The shake flask medium is prepared according to Verduyn (Verduyn, et al., 1992, Yeast. Vol. 8, 501-517, which is hereby incorporated by reference in its entirety), with the exception of substituting manganese tetrahydrate with manganese dihydrate. The medium is supplemented with D-glucose to target an initial D-glucose concentration. For example, the medium is supplemented with 250 grams of D-glucose per liter of media. To evaluate L-lactate consumption only, sodium L-lactate (e.g., Sigma; catalog number L7022) is used. To evaluate D-lactate consumption only, sodium D-lactate (e.g., Sigma; catalog number 71716) is used. To evaluate a mixture of D- and L-lactate, a mixture of about 50% D-lactate and 50% L-lactate is used. The pH of the media is adjusted to pH 4.5, and sterile filtered prior to use. The inoculated flask is incubated at 30° C. with shaking in an orbital shake at 75 rpm for at least 40 hours. Samples are taken and analyzed for glucose, ethanol, and lactate concentration in the broth during fermentation using high performance liquid chromatography with a refractive index detector.

A lactate consumption rate is calculated between two time points: the time of inoculation (to) and another time point later in the fermentation (t₁). The time t₁ is a measure of hours (h) after inoculation. Samples are taken at these two time points and the lactate concentration in both samples is measured. The measured lactate concentration in the sample taken at to is designated [HLA]₀ and has units of (gL⁻¹). Likewise, the measured lactate concentration in the sample taken at t₁ is designated [HLA]₁ and has units of (gL⁻¹).

The lactate consumption rate is then calculated as follows resulting in units of (gL⁻¹h⁻¹):

Lactate consumption rate=([HLA]₁−[HLA]₀)/t ₁

When D-lactate is measured, the calculation will yield a D-lactate consumption rate. Likewise, when L-lactate is measured, the calculation will yield a L-lactate consumption rate and when total lactate is measured, the calculation will yield a total lactate consumption rate.

For example, a shake flask experiment is sampled at inoculation (t₀=0 h) and 48 hours later (t₁=48 h). The total lactate in both samples is measured with the following results: [HLA]₀=25.0 gL⁻¹; and [HLA]₁=15.9 gL⁻¹. Then total lactate consumption rate is calculated as follows:

(25.0−15.9)/48=0.190 gL⁻¹h⁻¹.

The total lactate consumption rate is 0.190 gL⁻¹h⁻¹.

Example 1: Generation of Amylolytic Saccharomyces cerevisiae Strains

Described below are genetically modified Saccharomyces cerevisiae yeast strains. The strains described include strains having genetic modifications that improve the lactate-consuming ability of ethanol producing yeasts.

Strain 1-3: ura3Δ Saccharomyces cerevisiae Base Strain

Strain 1 (Ethanol Red™) is transformed with SEQ ID NO: 1. SEQ ID NO: 1 contains the following elements: i) an expression cassette for a mutant version of a 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase gene from Saccharomyces cerevisiae (ARO4-OFP); and ii) flanking DNA for targeted chromosomal integration into the URA3 locus. Transformants were selected on synthetic complete media containing 3.5 g/L of p-fluorophenylalanine, and 1 g/L L-tyrosine (ScD-PFP). Resulting transformants were streaked for single colony isolation on ScD-PFP. A single colony was selected. Correct integration of SEQ ID NO: 1 into one allele of locus A was verified by PCR in the single colony. A PCR verified isolate was designated Strain 1-1.

Stain 1-1 was transformed with SEQ ID NO: 2. SEQ ID NO: 2 contains the following elements: i) an expression cassette for an acetamidase (amdS) gene from Aspergillus nidulans; and ii) flanking DNA for targeted chromosomal integration into the URA3 locus. Transformants were selected on Yeast Nitrogen Base (without ammonium sulfate or amino acids) containing 80 mg/L uracil and 1 g/L acetamide as the sole nitrogen source. Resulting transformants were streaked for single colony isolation on Yeast Nitrogen Base (without ammonium sulfate or amino acids) containing 80 mg/L uracil and 1 g/L acetamide as the sole nitrogen source. A single colony was selected. Correct integration of SEQ ID NO: 2 into the second allele of locus A was verified by PCR in the single colony. A PCR verified isolate is designated Strain 1-2.

Strain 1-2 was co-transformed with SEQ ID NO: 3 and SEQ ID NO: 4. SEQ ID NO:3 contains the following elements: i) an open reading frame for a cre recombinase from P1 bacteriophage, and ii) flanking DNA homologous to SEQ ID NO:4. SEQ ID NO: 4 contains the following elements: i) a 2μ origin of replication; ii) a URA3 selectable marker from Saccharomyces cerevisiae; and iii) flanking DNA containing a PGK promoter and CYC1 terminator from Saccharomyces cerevisiae. Transformants were selected on synthetic dropout media lacking uracil (ScD-Ura). Resulting transformants were streaked for single colony isolation on ScD-Ura. A single colony was selected. The isolated colony was screened for growth on ScD-PFP and Yeast Nitrogen Base (without ammonium sulfate or amino acids) containing 80 mg/L uracil and 1 g/L acetamide as the sole nitrogen source. Loss of the ARO4-OFP and amdS genes was verified by PCR. The PCR verified isolate was streaked to YNB containing 5-FOA to select for loss of the 2μ plasmid. The PCR verified isolate was designated Strain 1-3.

Strain 1-4: Saccharomyces cerevisiae Expressing Two Codon Optimized Variants of the Saccharomycopsis fibuligera Glucoamylase at One Allele of CYB2

Strain 1-3 was co-transformed with SEQ ID NO: 5 and SEQ ID NO: 6. SEQ ID NO:5 contains the following elements: i) DNA homologous to the 5′ region of the native CYB2 gene; and ii) an expression cassette for a unique codon optimized variant of the Saccharomycopsis fibuligera glucoamylase, under control of the TDH3 promoter and CYC1 terminator; and iii) the URA3 promoter as well as a portion of the URA3 gene. SEQ ID NO: 6 contains the following elements: i) a portion of the URA3 gene and terminator; and ii) an expression cassette for a unique codon optimized variant of the Saccharomycopsis fibuligera glucoamylase, under control of the PGK promoter and RPL3 terminator; and iii) DNA homologous to the 3′ region of the native CYB2 gene. Transformants were selected on ScD-Ura. Resulting transformants were streaked for single colony isolation on ScD-Ura. A single colony was selected. Correct integration of SEQ ID NO: 5 and SEQ ID NO: 6 at one allele of CYB2 was verified by PCR. The PCR verified isolate was designated Strain 1-4.

Strain 1-5: Saccharomyces cerevisiae Expressing Four Codon Optimized Variants of the Saccharomycopsis fibuligera Glucoamylase at Both Alleles of CYB2

Strain 1-4 was co-transformed with SEQ ID NO: 7 and SEQ ID NO: 8. SEQ ID NO: 7 contains the following elements: i) DNA homologous to the 5′ region of the native CYB2 gene; and ii) an expression cassette for a unique codon optimized variant of the Saccharomycopsis fibuligera glucoamylase, under control of the TDH3 promoter and CYC1 terminator; and iii) the TEF1 promoter and a portion of the Aspergillus nidulans acetamidase gene (amdS). SEQ ID NO: 8 contains the following elements: i) a portion of the Aspergillus nidulans acetamidase gene (amdS) and ADH1 terminator; and ii) an expression cassette for a unique codon optimized variant of the Saccharomycopsis fibuligera glucoamylase, under control of the PGK promoter and RPL3 terminator; and iii) DNA homologous to the 3′ region of the native CYB2 gene. Transformants were selected on Yeast Nitrogen Base (without ammonium sulfate or amino acids) containing 80 mg/L uracil and 1 g/L acetamide as the sole nitrogen source. Resulting transformants were streaked for single colony isolation on Yeast Nitrogen Base (without ammonium sulfate or amino acids) containing 80 mg/L uracil and 1 g/L acetamide as the sole nitrogen source. A single colony was selected. Correct integration of SEQ ID NO: 7 and SEQ ID NO: 8 at the remaining allele of CYB2 was verified by PCR. The PCR verified isolate was designated Strain 1-5.

Strain 1-6: Recycling the URA3 and amdS Markers Via Cre Recombinase in Strain 1-5

Strain 1-5 was transformed with SEQ ID NO: 9. SEQ ID NO: 9 contains the following elements: i) an expression cassette for a mutant version of a 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase gene from Saccharomyces cerevisiae (ARO4-OFP); 2) an expression cassette for a cre recombinase from P1 bacteriophage; 3) an expression cassette containing the native URA3, and 4) the Saccharomyces cerevisiae CEN6 centromere. Transformants were selected on synthetic complete media containing 3.5 g/L of p-fluorophenylalanine, and 1 g/L L-tyrosine (ScD-PFP). Resulting transformants were streaked for single colony isolation on ScD-PFP. A single colony was selected. The PCR verified isolate was designated Strain 1-6.

Strain 1-8: Transformation of Strain 1-6 with Two Copies of the Saccharomyces cerevisiae IMA1 and Two Copies of the Saccharomyces mikatae MAL11-1.

Strain 1-6 was transformed with SEQ ID NO: 10. SEQ ID NO: 10 contains 5′ homology to integration locus C, an expression cassette for the ScIMA1, an expression cassette for the URA3 marker, an expression cassette for the SmMAL11-1, and 3′ homology to integration locus C locus. Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. A single colony is selected. Presence of the integration at locus C is verified by PCR. The PCR verified isolate is saved as Strain 1-7.

Strain 1-7 was transformed with SEQ ID NO: 11. SEQ ID NO: 11 contains 5′ homology to integration locus C, an expression cassette for the ScIMA1, an expression cassette for the Aspergillus nidulans acetamidase gene (amdS), an expression cassette for the SmMAL11-1, and 3′ homology to the integration locus C. Transformants were selected on Yeast Nitrogen Base (without ammonium sulfate or amino acids) containing 1 g/L acetamide as the sole nitrogen source. Resulting transformants were streaked for single colony isolation on Yeast Nitrogen Base (without ammonium sulfate or amino acids) containing 1 g/L acetamide as the sole nitrogen source. A single colony was selected. Correct integration of SEQ ID NO: 11 at the remaining allele of locus C was verified by PCR. The PCR verified isolate was designated Strain 1-8.

Strain 1-9: Recycling the URA3 and amdS Markers Via Cre Recombinase in Strain 1-8

Strain 1-8 was transformed with SEQ ID NO: 9. SEQ ID NO: 9 contains the following elements: i) an expression cassette for a mutant version of a 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase gene from Saccharomyces cerevisiae (ARO4-OFP); 2) an expression cassette for a cre recombinase from P1 bacteriophage; 3) an expression cassette containing the native URA3, and 4) the Saccharomyces cerevisiae CEN6 centromere. Transformants were selected on synthetic complete media containing 3.5 g/L of p-fluorophenylalanine, and 1 g/L L-tyrosine (ScD-PFP). Resulting transformants were streaked for single colony isolation on ScD-PFP. A single colony was selected. The PCR verified isolate was designated Strain 1-9.

Strain 1-10: Restoring the Native URA3 at the Original Locus in Strain 1-9

Strain 1-9 was transformed with SEQ ID NO: 12. SEQ ID NO: 12 contains the follow elements: 1) an expression cassette for the native URA3, with 5′ and 3′ homology to the disrupted URA3 locus in Strain 1-6. Transformants were selected on ScD-ura. Resulting transformants were streaked for single colony isolate on ScD-ura. A single colony was selected. The PCR verified isolate was designated Strain 1-10.

Strain 1-11 Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and a Saccharomyces cerevisiae Cytochrome b2.

Strain 1-9 is co-transformed with SEQ ID NO: 13 (pGPL5) and SEQ ID NO: 14 (pGPL7). SEQ ID NO: 13 contains the following elements in order: 1) flanking sequence corresponding to the upstream region of the S. cerevisiae CAN1 gene 2) an expression cassette containing a TDH3 promoter, Saccharomyces cerevisiae cytochrome b2 (CYB2) in SEQ ID NO: 15 and CYC1 terminator, and 3) loxP recombination sequence and the 5′ portion of an expression cassette for an orotidine-5′-phosphate decarboxylase (URA3). SEQ ID NO: 14 contains the following elements in order: 1) the 3′ portion of an expression cassette for an orotidine-5′-phosphate decarboxylase (URA3) and a loxP recombination sequence, 2) a cassette containing an ADH1 promoter and GAL10 terminator, and 4) flanking sequence corresponding to the downstream region of the S. cerevisiae CAN1 gene. Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-11.

Strain 1-12: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and an Issatchenkia orientalis Cytochrome b2.

Strain 1-9 is co-transformed with SEQ ID NO: 14 and SEQ ID NO: 16. SEQ ID NO: 16 is similar to SEQ ID NO: 13 with the following difference: the Saccharomyces cerevisiae cytochrome b2 gene in SEQ ID NO: 13 is replaced with the Issatchenkia orientalis cytochrome b2 (SEQ ID NO: 17). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-12.

Strain 1-13: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and an Aspergillus niger Lactic Oxidase.

Strain 1-9 is co-transformed with SEQ ID NO: 14 and SEQ ID NO: 18. SEQ ID NO: 18 is similar to SEQ ID NO: 13 with the following difference: the Saccharomyces cerevisiae cytochrome b2 gene in SEQ ID NO: 13 is replaced with the Aspergillus niger lactic oxidase with the C-terminal perixosomal targeting sequence removed (SEQ ID NO: 19). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-13.

Strain 1-14: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and a Yarrowia lipolytica Lactic Oxidase.

Strain 1-9 is co-transformed with SEQ ID NO: 14 and SEQ ID NO: 20. SEQ ID NO: 20 is similar to SEQ ID NO: 13 with the following difference: the Saccharomyces cerevisiae cytochrome b2 gene in SEQ ID NO: 13 is replaced with the Yarrowia lipolytica lactic oxidase with the C-terminal perixosomal targeting sequence removed SEQ ID NO: 21. Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-14.

Strain 1-15: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and an Issatchenkia orientalis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 22 (pGPL6) and SEQ ID NO: 23 (pESL4). SEQ ID NO: 22 contains the following elements in order: 1) flanking sequence corresponding to the upstream region of the S. cerevisiae CAN1 gene 2) a cassette containing a TDH3 promoter, and CYC1 terminator, and 3) loxP recombination sequence and the 5′ portion of an expression cassette for an orotidine-5′-phosphate decarboxylase (URA3). SEQ ID NO: 23 contains the following elements in order: 1) the 3′ portion of an expression cassette for an orotidine-5′-phosphate decarboxylase (URA3) and a loxP recombination sequence, 2) an expression cassette containing an ADH1 promoter, Issatchenkia orientalis monocarboxylate/proton symporter (JEN1) found in SEQ ID NO: 24, and a GAL10 terminator, and 4) flanking sequence corresponding to the downstream region of the S. cerevisiae CAN1 gene. Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-15.

Strain 1-16: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and a Saccharomyces cerevisiae Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 22 and SEQ ID NO: 25 (pESL1). SEQ ID NO: 25 is similar to SEQ ID NO: 23 with the following difference: the Issatchenkia orientalis monocarboxylate/proton symporter gene (JEN1) in SEQ ID NO: 23 is replaced with the Saccharomyces cerevisiae monocarboxylate/proton symporter (JEN1) gene (SEQ ID NO: 26). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-16.

Strain 1-17: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 22 and SEQ ID NO: 27 (pESL7). SEQ ID NO: 27 is similar to SEQ ID NO: 23 with the following difference: the Issatchenkia orientalis monocarboxylate/proton symporter gene (JEN1) in SEQ ID NO: 23 is replaced with the Kluyveromyces lactis monocarboxylate/proton symporter (JEN1) gene (SEQ ID NO: 28). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-17.

Strain 1-18: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and a Saccharomyces cerevisiae Acetate Transporter (ADY2^(Leu219Val, Ala252Gly)).

Strain 1-9 is co-transformed with SEQ ID NO: 22 and SEQ ID NO: 29 (pESL8). SEQ ID NO: 29 is similar to SEQ ID NO: 23 with the following difference: the Issatchenkia orientalis monocarboxylate/proton symporter gene (JEN1) in SEQ ID NO: 23 is replaced with the Saccharomyces cerevisiae acetate transporter (ADY2^(Leu219Val, Ala252Gly)) gene (SEQ ID NO: 30). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-18.

Strain 1-19: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and an Aggregatibacter actinomycetemcomitans LDH and a Saccharomyces cerevisiae Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 25 and SEQ ID NO: 31. SEQ ID NO: 31 is similar to SEQ ID NO: 13 with the following difference: the Saccharomyces cerevisiae cytochrome b2 gene in SEQ ID NO: 13 is replaced with the Aggregatibacter actinomycetemcomitans LDH (SEQ ID NO: 32). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-19.

Strain 1-20: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and an Ornithorhynchus anatinus LDH and a Saccharomyces cerevisiae Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 25 and SEQ ID NO: 33. SEQ ID NO: 33 is similar to SEQ ID NO: 13 with the following difference: the Saccharomyces cerevisiae cytochrome b2 gene in SEQ ID NO: 13 is replaced with the Ornithorhynchus anatinus LDH (SEQ ID NO: 34). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-20.

Strain 1-21: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and an Issatchenkia orientalis Cytochrome b2 and an Issatchenkia orientalis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 16 and SEQ ID NO: 23. Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-21.

Strain 1-22: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and an Issatchenkia orientalis Cytochrome b2 and a Saccharomyces cerevisiae Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 16 and SEQ ID NO: 25. Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-22.

Strain 1-23: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and an Issatchenkia orientalis Cytochrome b2 and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 16 and SEQ ID NO: 27. Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-23.

Strain 1-24: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and a Saccharomyces cerevisiae Cytochrome b2 and a Saccharomyces cerevisiae Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 13 and SEQ ID NO: 25. Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-24.

Strain 1-25: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and a Saccharomyces cerevisiae Cytochrome b2 and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 13 and SEQ ID NO: 27. Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-25.

Strain 1-26: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and an Aspergillus niger Lactic Oxidase and a Saccharomyces cerevisiae Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 18 and SEQ ID NO: 25. Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-26.

Strain 1-27: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and a Yarrowia lipolytica Lactic Oxidase and a Saccharomyces cerevisiae Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 20 and SEQ ID NO: 25. Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-27.

Strain 1-28: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and an Acetobacter aceti D-Lactic Oxidase and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 35 and SEQ ID NO: 27. SEQ ID NO: 35 is similar to SEQ ID NO: 13 with the following difference: the Saccharomyces cerevisiae cytochrome b2 gene in SEQ ID NO: 13 is replaced with the Acetobacter aceti D-lactic oxidase (SEQ ID NO: 36). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-28.

Strain 1-29: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and a Gluconobacter oxydans D-Lactic Oxidase and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 37 and SEQ ID NO: 27. SEQ ID NO: 37 is similar to SEQ ID NO: 13 with the following difference: the Saccharomyces cerevisiae cytochrome b2 gene in SEQ ID NO: 13 is replaced with the Gluconobacter oxydans D-lactic oxidase (SEQ ID NO: 38). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-29.

Strain 1-30: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and a Saccharomyces cerevisiae D-Lactic Dehydrogenase and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 39 and SEQ ID NO: 27. SEQ ID NO: 39 is similar to SEQ ID NO: 13 with the following difference: the Saccharomyces cerevisiae cytochrome b2 gene in SEQ ID NO: 13 is replaced with the Saccharomyces cerevisiae D-lactic dehydrogenase (SEQ ID NO: 40). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-30.

Strain 1-31: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and an Issatchenkia orientalis D-Lactic Dehydrogenase a and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 41 and SEQ ID NO: 27. SEQ ID NO: 41 is similar to SEQ ID NO: 13 with the following difference: the Saccharomyces cerevisiae cytochrome b2 gene in SEQ ID NO: 13 is replaced with the Issatchenkia orientalis D-lactic dehydrogenase (SEQ ID NO: 42). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-31.

Strain 1-32: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and an Issatchenkia orientalis D-Lactic Dehydrogenase B and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 43 and SEQ ID NO: 27. SEQ ID NO: 43 is similar to SEQ ID NO: 13 with the following difference: the Saccharomyces cerevisiae cytochrome b2 gene in SEQ ID NO: 13 is replaced with the Issatchenkia orientalis D-lactic dehydrogenase (SEQ ID NO: 44). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-32.

Strain 1-33: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and an Issatchenkia orientalis D-Lactic Dehydrogenase C and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 45 and SEQ ID NO: 27. SEQ ID NO: 45 is similar to SEQ ID NO: 13 with the following difference: the Saccharomyces cerevisiae cytochrome b2 in SEQ ID NO: 13 is replaced with the Issatchenkia orientalis D-lactic dehydrogenase (SEQ ID NO: 46). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-33.

Strain 1-34: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, Integration Locus Control.

Strain 1-9 is co-transformed with SEQ ID NO: 14 and SEQ ID NO: 22. Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-34.

Strain 1-35: Saccharomyces cerevisiae Expressing a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-3 is co-transformed with SEQ ID NO: 22 and SEQ ID NO: 27 (pESL7). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-35.

Strain 1-36: Saccharomyces cerevisiae Expressing a Saccharomyces cerevisiae Cytochrome b2 and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-3 is co-transformed with SEQ ID NO: 13 and SEQ ID NO: 27. Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-36.

Strain 1-37: Saccharomyces cerevisiae Expressing a Saccharomyces cerevisiae D-Lactic Dehydrogenase and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-3 is co-transformed with SEQ ID NO: 40 and SEQ ID NO: 27. Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-37.

Strain 1-38: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and a Lactobacillus fermentum Lactate Racemase and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 47 and SEQ ID NO: 27. SEQ ID NO: 47 is similar to SEQ ID NO: 13 with the following difference: the Saccharomyces cerevisiae cytochrome b2 in SEQ ID NO: 13 is replaced with the Lactobacillus fermentum lactate racemase (SEQ ID NO: 48). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-38.

Strain 1-39: Saccharomyces cerevisiae Expressing a Lactobacillus fermentum Lactate Racemase and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-3 is co-transformed with SEQ ID NO: 47 and SEQ ID NO: 27. Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-39.

Strain 1-40: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and a Saccharomyces cerevisiae Cytochrome b2 and a Saccharomyces cerevisiae Acetate Transporter (ADY2^(Leu219Val, Ala252Gly)).

Strain 1-9 is co-transformed with SEQ ID NO: 13 and SEQ ID NO: 29. Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-25.

Strain 1-41: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and 2 Copies of a Saccharomyces cerevisiae Cytochrome b2 and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-25 was transformed with SEQ ID NO: 49 and SEQ ID NO: 50. SEQ ID NO: 49 contains the following elements in order: 1) flanking sequence corresponding to the upstream region of the S. cerevisiae CAN1, 2) a cassette containing a TDH3 promoter, the Saccharyomyces cerevisiae CYB2, and CYC1 terminator, and 3) loxP recombination sequence and the 5′ portion of the expression cassette for the Aspergillus nidulans acetamidase gene (amdS). SEQ ID NO: 50 contains the following elements in order: 1) the 3′ portion of an expression cassette for the Aspergillus nidulans acetamidase (amdS), and a loxP recombination sequence, 2) an expression cassette containing an ADH1 promoter, Kluyveromyces lactis monocarboxylate/proton symporter (JEN1), and a GAL10 terminator, and 4) flanking sequence corresponding to the downstream region of the S. cerevisiae CAN1. Transformants were selected on Yeast Nitrogen Base (without ammonium sulfate or amino acids) containing 1 g/L acetamide as the sole nitrogen source. Resulting transformants were streaked for single colony isolation on Yeast Nitrogen Base (without ammonium sulfate or amino acids) containing 1 g/L acetamide as the sole nitrogen source. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-41.

Strain 1-42: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and a Saccharomyces kluyveri Cytochrome b2 and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 53 and SEQ ID NO: 27. SEQ ID NO: 53 is similar to SEQ ID NO: 13 with the following difference: the Saccharomyces cerevisiae cytochrome b2 in SEQ ID NO: 13 is replaced with the Saccharomyces kluyveri cytochrome b2 (SEQ ID NO: 54). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-42.

Strain 1-43: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and a Saccharomyces bayanus Cytochrome b2 and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 55 and SEQ ID NO: 27. SEQ ID NO: 55 is similar to SEQ ID NO: 13 with the following difference: the Saccharomyces cerevisiae cytochrome b2 in SEQ ID NO: 13 is replaced with the Saccharomyces bayanus cytochrome b2 (SEQ ID NO: 56). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-43.

Strain 1-44: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and a Cytochrome b2 and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 57 and SEQ ID NO: 27. SEQ ID NO: 57 is similar to SEQ ID NO: 13 with the following difference: the Saccharomyces cerevisiae cytochrome b2 in SEQ ID NO: 13 is replaced with the Zygosaccharomyces rouxii cytochrome b2 (SEQ ID NO: 58). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-44.

Strain 1-45: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and a Kluyveromyces lactis Cytochrome b2 and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 59 and SEQ ID NO: 27. SEQ ID NO: 59 is similar to SEQ ID NO: 13 with the following difference: the Saccharomyces cerevisiae cytochrome b2 in SEQ ID NO: 13 is replaced with the Kluyveromyces lactis cytochrome b2 (SEQ ID NO: 60). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-45.

Strain 1-46: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and a Kluyveromyces Dobzhanskii Cytochrome b2 and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 61 and SEQ ID NO: 27. SEQ ID NO: 61 is similar to SEQ ID NO: 13 with the following difference: the Saccharomyces cerevisiae cytochrome b2 gene in SEQ ID NO: 13 is replaced with the Kluyveromyces dobzhanskii cytochrome b2 (SEQ ID NO: 62). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-46.

Strain 1-47: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and a Saccharomyces kluyveri D-Lactic Dehydrogenase and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 63 and SEQ ID NO: 27. SEQ ID NO: 63 is similar to SEQ ID NO: 13 with the following difference: the Saccharomyces cerevisiae cytochrome b2 in SEQ ID NO: 13 is replaced with the Saccharomyces kluyveri D-lactic dehydrogenase (SEQ ID NO: 64). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-47.

Strain 1-48: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and a Saccharomyces bayanus D-Lactic Dehydrogenase and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 65 and SEQ ID NO: 27. SEQ ID NO: 63 is similar to SEQ ID NO: 13 with the following difference: the Saccharomyces cerevisiae cytochrome b2 in SEQ ID NO: 13 is replaced with the Saccharomyces bayanus D-lactic dehydrogenase (SEQ ID NO: 66). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-48.

Strain 1-49: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and an Aspergillus fumigatus D-Lactic Dehydrogenase and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 67 and SEQ ID NO: 27. SEQ ID NO: 67 is similar to SEQ ID NO: 13 with the following difference: the Saccharomyces cerevisiae cytochrome b2 in SEQ ID NO: 13 is replaced with the Aspergillus fumigatus D-lactic dehydrogenase (SEQ ID NO: 68). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-49.

Strain 1-50: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and a Kluyveromyces lactis D-Lactic Dehydrogenase and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 69 and SEQ ID NO: 27. SEQ ID NO: 69 is similar to SEQ ID NO: 13 with the following difference: the Saccharomyces cerevisiae cytochrome b2 in SEQ ID NO: 13 is replaced with the Kluyveromyces lactis D-lactic dehydrogenase (SEQ ID NO: 70). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-50.

Strain 1-51: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and a Kluyveromyces Dobzhanskii D-Lactic Dehydrogenase and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 71 and SEQ ID NO: 27. SEQ ID NO: 71 is similar to SEQ ID NO: 13 with the following difference: the Saccharomyces cerevisiae cytochrome b2 in SEQ ID NO: 13 is replaced with the Kluyveromyces dobzhanskii D-lactic dehydrogenase (SEQ ID NO: 72). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-51.

Strain 1-52: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and a Kluyveromyces marxianus D-Lactic Dehydrogenase and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 73 and SEQ ID NO: 27. SEQ ID NO: 73 is similar to SEQ ID NO: 13 with the following difference: the Saccharomyces cerevisiae cytochrome b2 in SEQ ID NO: 13 is replaced with the Kluyveromyces marxianus D-lactic dehydrogenase (SEQ ID NO: 74). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-52.

Strain 1-53: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and a Saccharomyces cerevisiae D-Lactic Dehydrogenase, a Saccharomyces cerevisiae Cytochrome b2, and a Kluyveromyces Dobzhanskii Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 80 and SEQ ID NO: 75. SEQ ID NO: 80 contains the following elements in order: 1) flanking sequence corresponding to the upstream region of the S. cerevisiae CAN1 2) an expression cassette containing a PGK promoter, Saccharomyces cerevisiae D-lactic dehydrogenase (DLD1) in SEQ ID NO: 40 and RPL3 terminator 3) an expression cassette containing a TDH3 promoter, Saccharomyces cerevisiae cytochrome b2 (CYB2) in SEQ ID NO: 15 and CYC1 terminator, and 4) loxP recombination sequence and the 5′ portion of an expression cassette for an orotidine-5′-phosphate decarboxylase (URA3). SEQ ID NO: 75 is similar to SEQ ID NO: 23 with the following difference: the Issatchenkia orientalis monocarboxylate/proton symporter (JEN1) in SEQ ID NO: 23 is replaced with the Kluyveromyces dobzhanskii monocarboxylate/proton symporter (JEN1) protein (SEQ ID NO: 76). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-53.

Strain 1-54: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and a Saccharomyces cerevisiae D-Lactic Dehydrogenase, a Saccharomyces cerevisiae Cytochrome b2, and a Kluyveromyces marxianus Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 80 and SEQ ID NO: 77. SEQ ID NO: 77 is similar to SEQ ID NO: 23 with the following difference: the Issatchenkia orientalis monocarboxylate/proton symporter (JEN1) in SEQ ID NO: 23 is replaced with the Kluyveromyces marxianus monocarboxylate/proton symporter (JEN1) (SEQ ID NO: 78). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-54.

Strain 1-55: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and a Saccharomyces cerevisiae D-Lactic Dehydrogenase, a Saccharomyces cerevisiae Cytochrome b2, and a Yarrowia lypolitica Monocarboxylate/Proton Symporter (JEN6).

Strain 1-9 is co-transformed with SEQ ID NO: 80 and SEQ ID NO: 79. SEQ ID NO: 79 is similar to SEQ ID NO: 23 with the following difference: the Issatchenkia orientalis monocarboxylate/proton symporter (JEN1) in SEQ ID NO: 23 is replaced with the Yarrowia lypolitica monocarboxylate/proton symporter (JEN6) (SEQ ID NO: 52). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-55.

Strain 1-56: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and a Saccharomyces cerevisiae D-Lactic Dehydrogenase, a Saccharomyces cerevisiae Cytochrome b2, and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 80 and SEQ ID NO: 27. Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-56.

Strain 1-57: Saccharomyces cerevisiae Expressing a Modified Saccharomycopsis fibuligera Glucoamylase, a Saccharomyces cerevisiae Isomaltase and a Saccharomyces mikatae Maltose Transporter, and Two Copies of a Saccharomyces cerevisiae D-Lactic Dehydrogenase, a Saccharomyces cerevisiae Cytochrome b2, and a Kluyveromyces lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-56 is co-transformed with SEQ ID NO: 81 and SEQ ID NO: 50. SEQ ID NO: 81 is similar to SEQ ID NO: 80 with the difference being that the 5′ portion of the URA3 marker is replaced with the 5′ portion of the amdS marker. Transformants are selected on YNB+acetamide plates. Resulting transformants are streaked for single colony isolation on YNB+acetamide plates. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-57.

Strain 1-58: S. cerevisiae Expressing a Modified S. fibuligera Glucoamylase, a S. cerevisiae Isomaltase and a S. mikatae Maltose Transporter, and a S. cerevisiae D-Lactic Dehydrogenase, a S. cerevisiae Cytochrome b2, and a S. cerevisiae Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 80 and SEQ ID NO: 25. Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-58.

Strain 1-59: S. cerevisiae Expressing a Modified S. fibuligera Glucoamylase, a S. cerevisiae Isomaltase and a S. mikatae Maltose Transporter, and a S. cerevisiae D-Lactic Dehydrogenase, a S. cerevisiae Cytochrome b2, and a S. bayanus Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 80 and SEQ ID NO: 82. SEQ ID NO: 82 is similar to SEQ ID NO: 50 with the following difference: the K. lactis JEN1 in SEQ ID NO: 50 is replaced with the S. bayanus JEN1 (SEQ ID NO: 83). Transformants are selected on ScD-Ura. Resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-59.

Strain 1-60: S. cerevisiae Expressing a Modified S. fibuligera Glucoamylase, a S. cerevisiae Isomaltase and a S. mikatae Maltose Transporter, and a S. cerevisiae D-Lactic Dehydrogenase, a S. cerevisiae Cytochrome b2, and a K. lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 80 and SEQ ID NO: 84. SEQ ID NO: 84 is similar to SEQ ID NO: 27 with the difference being that the ADH1 promoter SEQ ID NO: 27 is replaced with the GPD1 promoter. Transformants are selected on ScD-Ura, and the resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR.

Three independent transformants that were confirmed by PCR to contain a single copy of the expression cassette, were transformed for the second copy of the expression cassette using SEQ ID NO: 81 and SEQ ID NO: 87. SEQ ID NO: 87 is similar to SEQ ID NO: 50 with the difference being that the ADH1 promoter in SEQ ID NO: 50 is replaced with the GPD1 promoter. Transformants are selected on YNB+acetamide plates. Resulting transformants are streaked for single colony isolation on YNB+acetamide plates. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-60.

Strain 1-61: S. cerevisiae Expressing a Modified S. fibuligera Glucoamylase, a S. cerevisiae Isomaltase and a S. mikatae Maltose Transporter, and a S. cerevisiae D-Lactic Dehydrogenase, a S. cerevisiae Cytochrome b2, and a K. lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 80 and SEQ ID NO: 85. SEQ ID NO: 85 is similar to SEQ ID NO: 27 with the difference being that the ADH1 promoter SEQ ID NO: 27 is replaced with the ADH2 promoter. Transformants are selected on ScD-Ura, and the resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR.

Three independent transformants that were confirmed by PCR to contain a single copy of the expression cassette, were transformed for the second copy of the expression cassette using SEQ ID NO: 81 and SEQ ID NO: 88. SEQ ID NO: 88 is similar to SEQ ID NO: 50 with the difference being that the ADH1 promoter in SEQ ID NO: 50 is replaced with the ADH2 promoter. Transformants are selected on YNB+acetamide plates. Resulting transformants are streaked for single colony isolation on YNB+acetamide plates. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-61.

Strain 1-62: S. cerevisiae Expressing a Modified S. fibuligera Glucoamylase, a S. cerevisiae Isomaltase and a S. mikatae Maltose Transporter, and a S. cerevisiae D-Lactic Dehydrogenase, a S. cerevisiae Cytochrome b2, and a K. lactis Monocarboxylate/Proton Symporter (JEN1).

Strain 1-9 is co-transformed with SEQ ID NO: 80 and SEQ ID NO: 86. SEQ ID NO: 86 is similar to SEQ ID NO: 27 with the difference being that the ADH1 promoter SEQ ID NO: 27 is replaced with the PDC1 promoter. Transformants are selected on ScD-Ura, and the resulting transformants are streaked for single colony isolation on ScD-Ura. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR.

Three independent transformants that were confirmed by PCR to contain a single copy of the expression cassette, were transformed for the second copy of the expression cassette using SEQ ID NO: 81 and SEQ ID NO: 89. SEQ ID NO: 89 is similar to SEQ ID NO: 50 with the difference being that the ADH1 promoter in SEQ ID NO: 50 is replaced with the PDC1 promoter. Transformants are selected on YNB+acetamide plates. Resulting transformants are streaked for single colony isolation on YNB+acetamide plates. Single colonies are selected, and the correct integration of the expression cassette is confirmed by PCR. Three independent transformants are tested in a shake flask fermentation and a representative isolate is designated Strain 1-62.

TABLE 1 Summary Descriptions of Engineered Yeast Strain Parent Description Strain 1 N/A Saccharomyces cerevisiae (Lasaffre, Ethanol Red) Strain 1-1 Strain 1 ura3Δ/URA3, ARO4-OFP+ Strain 1-2 Strain 1-1 ura3Δ, ARO4-OFP+, amdS+ Strain 1-3 Strain 1-2 ura3Δ Strain 1-4 Strain 1-3 Saccharomycopsis fibuligera GLA1+; URA3+, Strain 1-5 Strain 1-4 Saccharomycopsis fibuligera GLA1+; URA3+, amdS+ Strain 1-6 Strain 1-5 Saccharomycopsis fibuligera GLA1+; ura3− Strain 1-7 Strain 1-6 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; URA3+ Strain 1-8 Strain 1-7 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; URA3+, amdS+ Strain 1-9 Strain 1-8 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; ura3− Strain 1-10 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; URA3+ Strain 1-11 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+: Saccharomyces cerevisae CYB2+; URA3+ Strain 1-12 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Issatchenkia orientalis CYB2+; URA3+ Strain 1-13 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Aspergillus niger L-LOX+; URA3+ Strain 1-14 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Yarrowia lipolytica L-LOX+; URA3+ Strain 1-15 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Issatchenkia orientalis JEN1+; URA3+ Strain 1-16 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Saccharomyces cerevisae JEN1+; URA3+ Strain 1-17 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Kluyveromyces lactis JEN1+; URA3+ Strain 1-18 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Saccharomyces cerevisae ADY2 (ADY2Leu219Val, Ala252Gly)+; URA3+ Strain 1-19 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Aggregatibacter actinomycetemcomitans LDH, Saccharomyces cerevisae JEN1+; URA3+ Strain 1-20 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Ornithorhynchus anatinus LDH, Saccharomyces cerevisae JEN1+; URA3+ Strain 1-21 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Issatchenkia orientalis CYB2+, Issatchenkia orientalis JEN1+; URA3+ Strain 1-22 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Issatchenkia orientalis CYB2+, Saccharomyces cerevisae JEN1+; URA3+ Strain 1-23 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Issatchenkia orientalis CYB2+, Kluyvromyces lactis JEN1+; URA3+ Strain 1-24 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Saccharomyces cerevisae CYB2+, Saccharomyces cerevisae JEN1+; URA3+ Strain 1-25 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Saccharomyces cerevisae CYB2+, Kluyveromyces lactis JEN1+; URA3+ Strain 1-26 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Aspergillus niger L-LOX, Saccharomyces cerevisae JEN1+; URA3+ Strain 1-27 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Yarrowia lipolytica L-LOX, Saccharomyces cerevisae JEN1+; URA3+ Strain 1-28 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; A. aceti D-LOX+, Kluyveromyces lactis JEN1+; URA3+ Strain 1-29 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Gluconobacter oxydans D-LOX+, Kluyveromyces lactis JEN1+; URA3+ Strain 1-30 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Saccharomyces cerevisae DLD1+, Kluyveromyces lactis JEN1+; URA3+ Strain 1-31 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Issatchenkia orientalis DLD1a+, Kluyveromyces lactis JEN1+; URA3+ Strain 1-32 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Issatchenkia orientalis DLD1b+, Kluyveromyces lactis JEN1+; URA3+ Strain 1-33 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Issatchenkia orientalis DLD1c+, Kluyveromyces lactis JEN1+; URA3+ Strain 1-34 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; CAN1 site control; URA3+ Strain 1-35 Strain 1-3 ura3Δ; Kluyveromyces lactis JEN1+; URA3+ Strain 1-36 Strain 1-3 ura3Δ; Saccharomyces cerevisae CYB2+, Kluyveromyces lactis JEN1+; URA3+ Strain 1-37 Strain 1-3 ura3Δ; Saccharomyces cerevisae DLD1+, Kluyveromyces lactis JEN1+; URA3+ Strain 1-38 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Lactobacillus fermentum lactate racemase+, Kluyveromyces lactis JEN1+; URA3+ Strain 1-39 Strain 1-3 ura3Δ; Lactobacillus fermentum lactate racemase+, Kluyveromyces lactis JEN1+; URA3+ Strain 1-40 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Saccharomyces cerevisae CYB2+, Saccharomyces cerevisae ADY2 (ADY2Leu219Val, Ala252Gly)+; URA3+ Strain 1-41 Strain 1-25 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; 2x Saccharomyces cerevisae CYB2+, 2x Kluyveromyces lactis JEN1+; URA3+ Strain 1-42 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Saccharomyces kluyveri CYB2+, Kluyveromyces lactis JEN1+; URA3+ Strain 1-43 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Saccharomyces bayanus CYB2+, Kluyveromyces lactis JEN1+; URA3+ Strain 1-44 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Zygosaccharomyces rouxii CYB2+, Kluyveromyces lactis JEN1+; URA3+ Strain 1-45 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Kluyveromyces lactis CYB2+, Kluyveromyces lactis JEN1+; URA3+ Strain 1-46 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Kluyveromyces dobzhanskii CYB2+, Kluyveromyces lactis JEN1+; URA3+ Strain 1-47 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Saccharomyces kluyveri DLD1+, Kluyveromyces lactis JEN1+; URA3+ Strain 1-48 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Saccharomyces bayanus DLD1+, Kluyveromyces lactis JEN1+; URA3+ Strain 1-49 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Aspergillus fumigatus DLD1+, Kluyveromyces lactis JEN1+; URA3+ Strain 1-50 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Kluyveromyces lactis DLD1+, Kluyveromyces lactis JEN1+; URA3+ Strain 1-51 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Kluyveromyces dobzhanskii DLD1+, Kluyveromyces lactis JEN1+; URA3+ Strain 1-52 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Kluyveromyces marxianus DLD1+, Kluyveromyces lactis JEN1+; URA3+ Strain 1-53 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Saccharyomyces cerevisiae DLD1+, Saccharyomyces cerevisiae CYB2+, Kluyveromyces dobzhanskii JEN1+; URA3+ Strain 1-54 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Saccharyomyces cerevisiae DLD1+, Saccharyomyces cerevisiae CYB2+, Kluyveromyces marxianus JEN1+; URA3+ Strain 1-55 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Saccharyomyces cerevisiae DLD1+, Saccharyomyces cerevisiae CYB2+, Yarrowia lypolitica JEN6+; URA3+ Strain 1-56 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Saccharyomyces cerevisiae DLD1+, Saccharyomyces cerevisiae CYB2+, Kluyveromyces lactis JEN1+; URA3+ Strain 1-57 Strain 1-56 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Saccharyomyces cerevisiae DLD1+, Saccharyomyces cerevisiae CYB2+, Kluyveromyces lactis JEN1+; URA3+ Strain 1-58 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Saccharyomyces cerevisiae DLD1+, Saccharyomyces cerevisiae CYB2+, Saccharyomyces cerevisiae JEN1+; URA3+ Strain 1-59 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Saccharyomyces cerevisiae DLD1+, Saccharyomyces cerevisiae CYB2+, Saccharyomyces bayanus JEN1+; URA3+ Strain 1-60 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Saccharyomyces cerevisiae DLD1+, Saccharyomyces cerevisiae CYB2+, Kluyveromyces lactis JEN1+; URA3+ Strain 1-61 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Saccharyomyces cerevisiae DLD1+, Saccharyomyces cerevisiae CYB2+, Kluyveromyces lactis JEN1+; URA3+ Strain 1-62 Strain 1-9 Saccharomycopsis fibuligera GLA1+; Saccharomyces cerevisae IMA1+, Saccharomyces mikatae MAL11+; Saccharyomyces cerevisiae DLD1+, Saccharyomyces cerevisiae CYB2+, Kluyveromyces lactis JEN1+; URA3+

Example 2: Evaluation of L-Lactate Consumption in Engineered Saccharomyces cerevisaie Strains Using an Ethanol Fermentation Shake Flask Assay

Described below are evaluations and associated data for ethanol fermentations run using selected yeast strains from Example 1. Strains 1 and 1-10 are reference strains used as comparators for various engineered strains. Strain 1 is a Saccharomyces cerevisiae yeast having commercially suitable ethanol tolerance. Strain 1-10 is a strain derived from strain 1 that is also suitable for commercial ethanol production.

Shake Flask Evaluation Using Defined Media.

Selected strains from those listed in Table 1 are streaked out on a ScD-Ura plate and incubated at 30° C. until single colonies are visible (1-2 days) or grown overnight in 4 ml of YP+100 g/L D-glucose in a 14 ml culture tube as a liquid culture at 30° C./250 rpm to generate seed biomass. A shake flask is inoculated with seed cell slurry to reach an initial OD₆₀₀ of 0.1-0.3 Immediately prior to inoculating, 60 mL of shake flask medium is added to a 250 mL non-baffled shake flask (Corning 4995-250) fitted with a screw cap containing a gas-permeable seal (corning 1395-45LTMC). The shake flask medium is prepared according to Verduyn (Verduyn, et al., 1992, Yeast. Vol. 8, 501-517), with the exception of substituting manganese tetrahydrate with manganese dihydrate. The medium is supplemented with D-glucose to target an initial D-glucose concentration of between 250 grams to 300 grams of D-glucose per liter of media. Additionally, the media is supplemented with sodium L-lactate (Sigma; catalog number L7022). The pH of the media is adjusted to pH 4.5, and sterile filtered prior to use.

The inoculated flask is incubated at 30° C. with shaking in an orbital shake at 75 rpm for at least 40 hours. Samples are taken and analyzed for glucose, ethanol and lactate concentration in the broth during fermentation using high performance liquid chromatography with a refractive index detector.

Example 2A: Evaluation of Overexpression of CYB2 in Strain 1-9

As shown in Table 2 below, a strain having a native CYB2 knocked-out (strain 1-10) does not appear to consume any L-lactate. The increase in L-lactate may be due to evaporation of water during the fermentation, resulting in a slight concentration increase. However, strains containing an overexpressed CYB2 (strains 1-11 and 1-12) perform similarly to a strain with a native CYB2 (Strain 1). Specifically, strains with a CYB2 consume very small amounts of L-Lactate while producing commercially significant ethanol amounts primarily by consuming glucose.

TABLE 2 L- Lactic acid consumption in a fermentation shake flask assay for Saccharomyces cerevisiae strains, including strains containing an overexpressed CYB2. Starting Concentration Mid-Point Concentration Final Concentration (g/L) (g/L) (g/L) (0 hours) (23 hours) (48 hours) L- L- L- Strain Glucose Ethanol Lactate Glucose Ethanol Lactate Glucose Ethanol Lactate Strain 256.1 0 2.9 57.4 84.6 2.8 0.9 110.7 2.5 1 Strain 256.1 0 2.9 57.7 84.4 3 1 111.8 3.1 1-10 Strain 256.1 0 2.9 56.5 85.7 2.7 0.6 111.5 2.5 1-11 Strain 256.1 0 2.9 61.4 83.2 2.7 1.3 111.7 2.5 1-12

Example 2B: Evaluation of Overexpression of CYB2 and S. cerevisiae JEN1 in Strain 1-9

As shown in Table 3 below, strains having both an overexpressed CYB2 and an overexpressed S. cerevisiae JEN1 (strains 1-22 and 1-24) show significant L-lactate consumption with a high amount of glucose still present in the fermentation broth. However, a strain having native CYB2 and JEN1 (strain 1) consumes L-lactate mostly only after the glucose concentration is very low, while strains having no CYB2 (strains 1-10, 1-16, and 1-34) do not consume L-lactate. FIGS. 1A-1C show data for strain 1-24 corresponding to a second fermentation shake flask run.

TABLE 3 L-lactate consumption in fermentation shake flask assays for Saccharomyces cerevisiae strains, including strains containing an overexpressed CYB2 and S. cerevisiae JEN1. Starting Concentration Mid-Point Concentration Final Concentration (g/L) (g/L) (g/L) (0 hours) (20 hours) (41 hours) L- L- L- Strain Glucose Ethanol Lactate Glucose Ethanol Lactate Glucose Ethanol Lactate Strain 254.9 0 5.2 111 60.6 5.1 0.2 110 4.4 1 Strain 254.9 0 5.2 110.3 61.2 5.3 0.3 111 5.4 1-10 Strain 254.9 0 5.2 123.2 53.1 5.2 0.4 105.7 5.4 1-16 Strain 254.9 0 5.2 100.9 63.5 4.8 0 110 4.5 1-22 Strain 254.9 0 5.2 98.4 63.5 4.7 0 110.2 4.3 1-24 Strain 254.9 0 5.2 111.5 59.6 5.2 0 109.7 5.3 1-34

Example 2C: Evaluation of Overexpression of CYB2 and Inclusion of Kl JEN1 and ScADY2 in Strain 1-9

As shown in Table 4 below, a strain having a native CYB2, JEN1, and ADY2 shows minimal L-lactate consumption in the presence of glucose. Strain having an overexpressed CYB2 and either an overexpressed JEN1 (strain 1-24) or an ADY2 with mutations (strain 1-40) show significantly higher L-lactate consumption in the presence of glucose. A strain having an overexpressed CYB2 and a K. lactis JEN1 (strain 1-25) has the highest L-lactate consumption. Further, strains 1-24, 1-25, and 1-40 show significantly higher ethanol titer than strain 1.

TABLE 4 L-lactate consumption in fermentation shake flask assays for Saccharomyces cerevisiae strains, including strains containing an overexpressed CYB2 and either a Klactis JEN1 or a ScADY2 with mutations. Mid-Point Concentration (g/L) Final Concentration (g/L) (20 hours) (41 hours) L- L- Starting Lactate Lactate Concentration (g/L) consumption consumption (0 hours) rate rate L- L- (gL⁻¹h⁻¹) L- (gL⁻¹h⁻¹) Strain Glucose EtOH Lactate Glucose EtOH Lactate 20 h Glucose EtOH Lactate 41 h Strain 308.5 0 5.7 209.3 60.6 5.1 0.029 52.1 109.4 5.3 0.010 1 Strain 308.5 0 5.7 202.6 61.2 5.3 0.020 40.6 114.1 6.1 −0.010 1-10 Strain 308.5 0 5.7 202.1 63.5 4.8 0.044 37.9 116 4.7 0.024 1-24 Strain 308.5 0 5.7 199.2 63.5 4.7 0.049 36.7 118 4 0.041 1-25 Strain 308.5 0 5.7 199.2 43.6 5.7 0.000 30.3 120.5 4.7 0.024 1-40

Example 2D: Evaluation of Overexpression of Lactic Oxidase in Strain 1-9

Strains with an overexpressed lactic oxidase (L-LOX) might be expected to show improved L-lactate consumption. However, as shown in Table 5 below, strains having an overexpressed L-LOX (strains 1-13 and 1-14) do not show improved L-lactate consumption versus the comparator strains.

TABLE 5 L-lactate consumption in Saccharomyces cerevisiae strains, including strains containing an overexpressed lactic oxidase in fermentation shake flask assays. Starting Concentration Mid-Point Concentration (g/L) (g/L) Final Concentration (g/L) (0 hours) (20 hours) (41 hours) L- L- L- Strain Glucose Ethanol Lactate Glucose Ethanol Lactate Glucose Ethanol Lactate Strain 254.9 0 5.2 111 60.6 5.1 0.2 110 4.4 1 Strain 254.9 0 5.2 110.3 61.2 5.3 0.3 111 5.4 1-10 Strain 254.9 0 5.2 112.1 59.5 5.2 0.2 109.8 5.3 1-13 Strain 254.9 0 5.2 104.7 62.1 5.2 0 110.9 5.3 1-14 Strain 254.9 0 5.2 111.5 59.6 5.2 0 109.7 5.3 1-34

Example 2E: Evaluation of Overexpression of Lactic Oxidase and an Overexpressed JEN1 in Strain 1-9

As discussed above, strains with an overexpressed lactic oxidase (L-LOX) might be expected to show improved L-lactate consumption, but do not show improved L-lactate consumption. Further, as shown in Table 6 below, strains having an overexpressed JEN1 (strains 1-26 and 1-27) and a L-LOX also do not show improved L-lactate consumption.

In addition, a strain having an I. orientalis CYB2 and an I. orientalis JEN1 (strain 1-21) exhibits the same L-lactate consumption as strain 1, but with lower ethanol production and glucose consumption, even though the parent wild-type organism (I. orientalis) can grow on L-lactate as a carbon source.

TABLE 6 L- lactate consumption in fermentation shake flask assays for Saccharomyces cerevisiae strains, including strains containing an overexpressed lactic oxidase and an overexpressed JEN1, and a strain having I. orientalis CYB2 and I. orientalis JEN1. Starting Concentration (g/L) Final Concentration (g/L) (0 hours) (41.3 hours) L- L- Strain Glucose Ethanol Lactate Glucose Ethanol Lactate Strain 307.1 0 5.5 17.9 120.5 4.5 1 Strain 307.1 0 5.5 25 116.8 5.5 1-10 Strain 307.1 0 5.5 53.7 99.7 5.4 1-16 Strain 307.1 0 5.5 28.8 112.9 4.5 1-21 Strain 307.1 0 5.5 20.4 116.5 5.5 1-26 Strain 307.1 0 5.5 20.2 114.8 5.6 1-27

Example 2F: Evaluation of Overexpression of a Lactate Dehydrogenase in Combination with a Sc JEN1 in Strain 1-9

Strains including an overexpressed lactate dehydrogenase might be expected to show improved L-lactate consumption, especially if anaerobic fermentation is expected. However, Table 7 shows that strains including a lactate dehydrogenase (LDH) (strains 1-19 and 1-20) actually produce L-lactate instead of consuming L-lactate.

TABLE 7 L-lactate consumption in fermentation shake flask assays for Saccharomyces cerevisiae strains, including strains containing an overexpressed lactate dehydrogenase and JEN1 transporter. Starting Concentration (g/L) Final Concentration (g/L) (0 hours) (41.3 hours) L- L- Strain Glucose Ethanol Lactate Glucose Ethanol Lactate Strain 1 307.1 0 5.5 17.9 120.5 4.5 Strain 307.1 0 5.5 25.0 116.8 5.5 1-10 Strain 307.1 0 5.5 29.0 106.4 15.4 1-19 Strain 307.1 0 5.5 100.7 67.7 33.3 1-20 Strain 307.1 0 5.5 53.7 99.7 5.4 1-16

Example 2G: Evaluation of Various Heterologous CYB2 Genes with K. lactis JEN1 in Strain 1-9

As shown in Table 8, a strain containing a Z. rouxii CYB2 (strain 1-44) or a K. lactis CYB2 (strain 1-45) showed higher L-lactate consumption and higher ethanol titer than the strain with a Sc CYB2. Strains with other CYB2 (1-42, 1-43, and 1-46) showed significant L-lactate consumption and commercially relevant ethanol titers.

TABLE 8 L-lactate consumption in fermentation shake flask assays for Saccharomyces cerevisiae strains, including strains containing an overexpressed CYB2 and K. lactis JEN1 Starting Concentration Mid-Point Concentration (g/L) (g/L) Final Concentration (g/L) (0 hours) (19.5 hours) (40 hours) L- L- L- Strain Glucose Ethanol Lactate Glucose Ethanol Lactate Glucose Ethanol Lactate Strain 282.0 0 5.5 157.3 53.8 5.5 2.3 126.6 4.7 1 Strain 282.0 0 5.5 165.0 53.9 5.8 9.9 122.5 5.7 1-10 Strain 282.0 0 5.5 149.7 59.4 5.2 8.0 125.1 5.6 1-17 Strain 282.0 0 5.5 144.3 59.8 5.0 0.6 128.2 3.9 1-25 Strain 282.0 0 5.5 151.3 58.8 4.5 4.6 126.8 3.1 1-42 Strain 282.0 0 5.5 147.4 57.8 5.1 6.5 126.8 4.1 1-43 Strain 282.0 0 5.5 143.1 59.5 4.6 2.0 129.0 3.0 1-44 Strain 282.0 0 5.5 149.3 57.1 4.4 2.4 129.1 3.0 1-45 Strain 282.0 0 5.5 151.3 58.3 4.6 6.6 126.7 3.5 1-46

Example 21—Evaluation of Various Heterologous Monocarboxylate/Proton Symporters in Strain 1-9

As shown in Table 9, two strains with Kluyveromyces JEN1 (K. dobzhanskii, strain 1-53; K. lactis, strain 1-56) showed the highest lactate consumption and ethanol titers. The strains including a Kluyveromyces marxianus JEN1 (strain 1-54) and Yarrowia lypolitica JEN6 (strain 1-55) also showed improved lactate consumption compared to reference strains.

TABLE 9 Total lactate consumption (mixture of L- and D-lactate) in fermentation shake flask assays for S. cerevisiae strains, including strains containing an overexpressed S. cerevisiae DLD1, S. cerevisiae CYB2, and JEN1 or JEN6. Starting Concentration Mid-Point Concentration (g/L) (g/L) Final Concentration (g/L) (0 hours) (19.5 hours) (40 hours) Total Total Total Strain Glucose Ethanol Lactate Glucose Ethanol Lactate Glucose Ethanol Lactate Strain 275.9 0.0 8.1 159.2 47.3 7.8 4.8 120.9 7.0 1 Strain 275.9 0.0 8.1 158.6 47.8 7.9 8.0 120.4 7.7 1-10 Strain 275.9 0.0 8.1 155.6 50.6 7.1 7.5 121.5 5.4 1-53 Strain 275.9 0.0 8.1 155.7 49.3 7.2 6.7 118.6 6.0 1-54 Strain 275.9 0.0 8.1 180.2 40.7 7.4 19.0 115.5 6.3 1-55 Strain 275.9 0.0 8.1 155.0 50.2 7.2 3.9 122.8 4.7 1-56

Example 3: Evaluation of D-Lactate Consumption in Engineered Saccharomyces cerevisiae Strains Using an Ethanol Fermentation Shake Flask Assay

Described below are evaluations and associated data for ethanol fermentations run using selected yeast strains from Example 1. Shake flask evaluation is performed as described in Example 2, except sodium D-lactate (Sigma; catalog number 71716) is used instead of sodium L-Lactate.

Example 3A: Evaluation of Overexpression of a JEN1 Transporter in Strain 1-9

As shown in Table 10 and FIGS. 2A-2C, a strain containing an overexpressed K. lactis JEN1 had significantly higher D-lactate consumption and also significantly higher ethanol titer than the reference strains (strains 1 and 1-10) or strains containing other overexpressed JEN1 genes (strains 1-15 and 1-16).

TABLE 10 D-lactate consumption in Saccharomyces cerevisiae strains, including strains containing an overexpressed JEN1 in fermentation shake flask assays. Mid-point Concentration (g/L) Final Concentration (g/L) (20.5 hours) (42 hours) D- D- Starting Lactate Lactate Concentration (g/L) Consumption Consumption (0 hours) rate rate D- D- gL⁻¹h⁻¹ D- gL⁻¹h⁻¹ Strain Glucose EtOH lactate Glucose EtOH Lactate 20.5 h Glucose EtOH Lactate 42 h Strain 1 309.1 0 3.6 169.8 51.1 3.5 0.005 15.5 117.9 3.0 0.014 Strain 309.1 0 3.6 167.9 54.6 3.5 0.005  9.2 125.8 3.1 0.012 1-10 Strain 309.1 0 3.6 165.2 52.9 3.4 0.010 29.8 116.8 2.9 0.017 1-15 Strain 309.1 0 3.6 187.5 44.6 3.4 0.010 52.1 102.0 3.0 0.014 1-16 Strain 309.1 0 3.6 161.6 53.0 2.9 0.034 15.1 131.7 1.9 0.041 1-17

Example 3B: Evaluation of Overexpression of a Saccharomyces cerevisae ADY2^((ADY2Leu219Val, Ala252Gly)) Permease in Strain 1-9

As shown in Table 11, D-lactate consumption and ethanol production are significantly higher in a strain containing a K. lactis JEN1 than in the reference strains, while a strain containing ADY2 (strain 1-18) shows performance similar to the reference strains.

TABLE 11 D-lactate consumption in Saccharomyces cerevisiae strains containing an overexpressed JEN1 in fermentation shake flask assays. Starting Concentration (g/L) Final Concentration (g/L) (0 hours) (42 hours) D- D- Strain Glucose Ethanol lactate Glucose Ethanol Lactate Strain 1 307.0 0 3.5 41.5 114.1 3.1 Strain 307.0 0 3.6 32.6 119.2 3.0 1-10 Strain 307.0 0 3.6 29.1 120.7 1.7 1-17 Strain 307.0 0 3.6 44.5 115.0 3.1 1-18

Example 3C: Evaluation of Overexpression of a D-Lactate Dehydrogenase and a K. lactis JEN1 in Strain 1-9

As shown in FIGS. 3A-3C, a strain containing a K Lactis JEN1 and an overexpressed DLD (strain 1-30) shows significantly improved D-lactate consumption and a higher ethanol titer than the reference strains. Further, the D-lactate consumption of strain 1-30 is significantly improved over a strain having only the K Lactis JEN1 (strain 1-17).

Example 3D: Evaluation of Issatchenkia orientalis D-Lactate Dehydrogenase and K. lactis JEN1 in Strain 1-9

Table 12 below shows data for three homolog strains containing a K Lactis JEN1 and an overexpressed I. orientalis DLD (strains 1-31, 1-32, and 1-33). Each of these three homologs shows improved D-lactate consumption compared to a reference strain (1-10).

TABLE 12 D- lactate consumption in fermentation shake flask assays of Saccharomyces cerevisiae strains containing an overexpressed D-lactate oxidase and a K. lactis JEN1. Starting Concentration Mid-point Concentration (g/L) (g/L) Final Concentration (g/L) (0 hours) (20.5 hours) (42 hours) D- D- D- Strain Glucose Ethanol lactate Glucose Ethanol Lactate Glucose Ethanol Lactate Strain 301.3 0 3.9 191.8 42.3 3.7 29.9 117.8 3.3 1-10 Strain 301.3 0 3.9 194.7 41.6 2.9 37.4 114.9 1.3 1-31 Strain 301.3 0 3.9 190.8 42.9 3.3 29.3 119.3 2.1 1-32 Strain 301.3 0 3.9 194.2 41.6 2.9 34.7 113.4 1.0 1-33

Example 3E: Evaluation of Overexpressed D-Lactate Oxidase and K. lactis JEN1 in Strain 1-9

As shown in Table 13 below, strains containing an overexpressed D-lactate oxidase (D-LOX) and a K. lactis JEN1 (strains 1-28 and 1-29) show improved D-lactate consumption compared to reference strains (strains 1 and 1-10), but show less D-lactate consumption than a strain containing only a K. lactis JEN1 (strain 1-17). A strain containing a D-LOX might be expected to show improved D-lactate consumption, however, as seen with the L-LOX strains described above, the inclusion of D-LOX does not improve the D-lactate consumption.

TABLE 13 D-lactate consumption in fermentation shake flask assays of Saccharomyces cerevisiae strains containing an overexpressed D-lactate oxidase and a K. lactis JEN1. Starting Concentration (g/L) Final Concentration (g/L) (0 hours) (42 hours) D- D- Strain Glucose Ethanol lactate Glucose Ethanol Lactate Strain 1 307.0 0 3.5 41.5 114.1 3.1 Strain 307.0 0 3.6 32.6 119.2 3.0 1-10 Strain 307.0 0 3.6 29.1 120.7 1.7 1-17 Strain 307.0 0 3.6 94.3  97.9 2.6 1-28 Strain 307.0 0 3.6 43.0 116.3 2.0 1-29

Example 3F: Evaluation of Various Heterologous DLD Genes with K. lactis JEN1 in Strain 1-9

As shown in Table 14, a strain containing a K. lactis DLD (1-50) had the highest ethanol titer and L-lactate consumption than other strains with selected DLDs. However, the other strains (1-47, 1-48, 1-49, 1-51, and 1-52) all showed significant D-lactate consumption and commercially relevant ethanol titers.

TABLE 14 D-lactate consumption in fermentation shake flask assays for Saccharomyces cerevisiae strains, including strains containing an overexpressed DLD1 and K. lactis JEN1. Starting Concentration Mid-Point Concentration (g/L) (g/L) Final Concentration (g/L) (0 hours) (19.5 hours) (40 hours) D- D- D- Strain Glucose Ethanol Lactate Glucose Ethanol Lactate Glucose Ethanol Lactate Strain 282.7 0.0 4.1 146.2 59.0 4.0 1.1 127.5 3.5 1 Strain 282.7 0.0 4.1 140.4 59.9 3.9 1.8 127.4 3.5 1-10 Strain 282.7 0.0 4.1 140.6 61.5 3.6 1.9 128.6 2.5 1-17 Strain 282.7 0.0 4.1 135.5 64.1 3.0 4.2 127.1 1.7 1-30 Strain 282.7 0.0 4.1 140.9 60.9 3.1 3.1 127.1 1.8 1-47 Strain 282.7 0.0 4.1 138.3 62.3 3.5 2.7 128.0 2.8 1-48 Strain 282.7 0.0 4.1 146.4 60.5 3.5 5.8 125.2 2.6 1-49 Strain 282.7 0.0 4.1 139.4 62.1 3.0 1.3 129.3 1.7 1-50 Strain 282.7 0.0 4.1 164.7 50.9 3.2 11.3 122.2 2.0 1-51 Strain 282.7 0.0 4.1 154.4 55.6 3.2 2.8 125.3 2.4 1-52

Example 4: Evaluation of a Genetically Modified Saccharomyces cerevisiae Strain in a Simultaneous Saccharification Fermentation (SSF) Shake Flask Assay

A Saccharomyces cerevisiae strain containing an overexpressed S. cerevisiae CYB2 and a Kluyvermyces lactis JEN1 is evaluated for consumption of lactic acid and D-glucose, and also production of ethanol. Strains obtained as described in Example 1.

Strains are struck to a ScD-ura plate and incubated at 25° C. until single colonies are visible (2-3 days). Cells from the ScD-ura plate are scraped into sterile shake flask medium and the optical density (OD₆₀₀) is measured. Optical density is measured at wavelength of 600 nm with a 1 cm path length using a model Genesys20 spectrophotometer (Thermo Scientific). A shake flask is inoculated with the cell slurry to reach an initial OD₆₀₀ of 0.1 Immediately prior to inoculating, 50 mL of shake flask medium is added to a 250 mL non-baffled shake flask (Corning 4995-250) fitted with a screw cap containing a gas-permeable seal (corning 1395-45LTMC). The shake flask medium consists of 850 g partially hydrolyzed corn starch, 150 g filtered light steep water, 10 g water, 25 g glucose, and 1 g urea. Duplicate flasks for each strain are incubated at 30° C. with shaking in an orbital shake at 100 rpm for 48 hours. Samples are taken and analyzed for metabolite concentrations in the broth during fermentation by HPLC with refractive index and UPLC with ELSD detection. Lactic acid (both D- and L-) is a component of the light steep water and is produced through contamination of the light steep water by lactic acid producing bacteria. The fraction of the D- and L-lactic acid in the light steep water varies between lots, and the absolute amount is not predictable. In general, the fraction of D- and L-lactic is a 50:50 racemic mix of the two enantiomers is at a total concentration of approximately 25 grams of lactic acid per liter of light steep water. Light steep water also contains low levels of glucose.

As shown in FIGS. 4A and 4B, a strain containing an overexpressed CYB2 and a K Lactis JEN1 (strain 1-25) consumes most or all of D,L-lactate while producing a similar amount of ethanol compared to the reference strains.

Example 5: Performance of Genetically Modified Yeast Strain in SSF with Relatively Low Levels of Glucose and Relatively High Levels of D,L-Lactate

Strain 1-41 is obtained as described in Example 1. Strain 1-41 is strain 1-9 containing 2 copies of the ScCYB2 and 2 copies of the KlJEN1. Strains are run in a shake flask fermentation according to Example 4, with the following differences: 1) the shake flask medium of this Example (Example 5) is light steep water; 2) the shake flasks are inoculated with a cell slurry to reach an initial OD₆₀₀ of 4.0; 3) the non-baffled shake flasks are fitted with a Morton cap; and 4) the flasks are incubated in an orbital shaker at 150 rpm.

As shown in Tables 15 and 16 and FIGS. 5A and 5B, the strain containing overexpression of ScCYB2 and also containing KlJEN1 (1-41) consumed significantly more D,L-lactate than the reference strains, while producing a significantly higher ethanol titer than the reference strains.

TABLE 15 Overexpression of a ScCYB2 and Kl JEN1 in Strain 1-9 in a simultaneous saccharification shake flask assay Starting Concentration (g/L) Mid-point Concentration (g/L) Final Concentration (g/L) (0 hours) (7 hours) (48 hours) Strain Glucose EtOH Lactate Glucose EtOH Lactate Glucose EtOH Lactate Strain 11.65 0.59 25 0 6.7 21.2 0 7.4 15.9 1 Strain 11.65 0.59 25 0 6.5 21.8 0 5.7 19.4 1-10 Strain 11.65 0.59 25 0.16 7.3 20.3 0 8.7 13.0 1-41

TABLE 16 Rate of total lactate consumption (D- and L-Lactate) Total Lactate consumption rate (g L⁻¹h⁻¹) Strain 0 to 7 hours 7 hours to 48 hours 0 to 48 hours Strain 1 0.543 0.129 0.190 Strain 1-10 0.457 0.059 0.117 Strain 1-41 0.671 0.178 0.250

Example 6: L-Lactate Consumption in Genetically Modified Yeast Strains with Selected Heterologous Monocarboxylic/Monocarboxylate Transporters

S. cerevisiae strains containing selected heterologous monocarboxylic/monocarboxylate transporters are evaluated for L-lactate transport/consumption. As shown previously, K. lactis JEN1 has a higher affinity for D-lactate transport compared to L-lactate transport. Shake flask assays are performed using defined media with only L-lactate present. Dextrose concentrations are not measured, but are expected to be about 150 g/L at 20 h.

As shown in Table 17 and FIG. 6, all heterologous monocarboxylic/monocarboxylate transporters tested exhibit improved L-lactate consumption compared to reference strains (strains 1 and 1-10).

TABLE 17 L-lactate consumption in fermentation shake flask assays for S. cerevisiae strains, including strains containing an overexpressed S. cerevisiae DLD1, S. cerevisiae CYB2, selected heterologous monocarboxylic/monocarboxylate transporters. Final Concentration (g/L) (41 hours) Strain Glucose Ethanol L-Lactate 1 0.2 130.8 1.3 1-10 0.2 130.7 2.9 1-53 0.2 132.3 0.4 1-54 0.2 131.4 1.0 1-55 0.3 133.3 1.0 1-56 0.2 132.1 0.6 1-58 0.1 131.8 0.8 1-59 0.2 132.1 0.8

Example 7: Performance of Genetically Modified Yeast Strain in Production-Scale Ethanol Fermentaion Process

A continuous fermentation process for producing ethanol is run on commercial scale using a reference strain with no lactic acid consumption pathway (strain 1-10) and (separately) a strain with an exogenous lactic consumption pathway enabled (strain 1-57) using an initial fermentation media including light steep water (LSW). Stage 1 is the propagator and Stage 2 is the pre-fermenter.

The changing concentration of D/L-lactic at the different stages reflects a number of changes to the composition of the fermentation broth due to inlet streams and dilution of the broth. Dilution levels are substantially the same for each strain at each stage. Therefore, relevant comparisons are the changing ratio of D/L-lactic for strain 1-10 vs. strain 1-57 within any given stage.

As shown in Table 18, a strain having a native CYB2 knocked-out and no exogenous lactic acid consumption pathway (strain 1-10) shows higher concentrations of both L- and D-lactic in each of Stage 1 and Stage 2, relative to a strain with the exogenous lactic consumption pathway enabled (strain 1-57).

TABLE 18 Lactate consumption by genetically modified yeast strains on production scale raw LSW Stage 1 Stage 2 Total Total Total L-lactic D-lactic Lactic L-lactic D-lactic Lactic L-lactic D-lactic Lactic (g/L) (g/L) (g/L) (g/L) (g/L) (g/L) (g/L) (g/L) (g/L) Strain 14.5 ± 2.7  9.8 ± 1.6 24.3 ± 4.1 7.8 ± 0.8 4.2 ± 1.8 12.0 ± 1.6 4.9 ± 0.3 2.1 ± 0.9 6.9 ± 0.3 1-10 Strain   13 ± 3.1 11.1 ± 3.4 24.1 ± 6.5 5.6 ± 0.7 1.7 ± 0.3  7.3 ± 0.3 3.9 ± 0.5 0.5 ± 0.8 4.4 ± 0.9 1-57

Example 8: Evaluation of Promoters for Driving Expression of a JEN1 Transporter

Alternative promoters to the promoter used in strain 1-57 (ADH1) are evaluated for driving expression of a JEN1 transporter. Strains were evaluated in a simultaneous saccharification fermentation (SSF) shake flask assay. These shake flasks serve as a proxy for assessing early fermentation burden of the selected strains.

In one aspect, as shown in Table 19, strains with alternative promoters to the promoter used in strain 1-57 (i.e., strains 1-60, 1-61, and 1-62) show significantly higher ethanol titers at the mid-point (22 h), therefore exhibiting reduced fermentation burden.

In another aspect, strain 1-57 is shown to generate significantly less glycerol with a corresponding significant increase in ethanol titer compared to all other strains. All strains with an enabled exogenous lactate-consumption pathway demonstrate lactate consumption and also the same or higher final ethanol titer compared to the reference strains. This demonstrates that strains with an enabled exogenous lactate-consumption pathway combined with selected promoters can achieve higher ethanol titers and/or the same ethanol titer at an earlier time point, either of which can provide a significant commercial advantage (i.e., increased throughput or reduced cycle time, or both).

TABLE 19 SSF shake flask assays for selected strains End Point Starting Concentration (g/L) Mid-Point Concentration (g/L) Concentration (g/L) (0 hours) (22 hours) (68 hours) Total Total Total Strain Glucose EtOH Glycerol Lactate Glucose EtOH Glycerol Lactate Glucose EtOH Glycerol Lactate Strain 34.4 0.2 0.1 2.4 37.6 73.8 6.6 2.5 0.6 150.4 9.3 1.5 1 Strain 34.4 0.2 0.1 2.4 22.1 71.7 5.6 2.8 0.0 150.3 8.6 2.2 1-10 Strain 34.4 0.2 0.1 2.4 15.8 67.7 4.3 2.0 0.0 154 7.3 0.0 1-57 Strain 34.4 0.2 0.1 2.4 18.6 73.2 5.4 2.1 0.0 152.6 8.2 0.2 1-60 Strain 34.4 0.2 0.1 2.4 23 74.2 5.7 2.5 0.0 150.3 8.6 0.8 1-61 Strain 34.4 0.2 0.1 2.4 18.4 74.3 5.1 2.0 0.0 151.6 7.8 0.0 1-62

Example 9: Batch SSF with Selected Strains

Strain 1-62 is benchmarked against Strain 1-10 in a lab scale batch fermentation process. The feedstock consists of a partially saccharified starch stream with a starting percent dextrose concentration between 20-35%. The starting pH is between 3.5 and 4.5 and the operating temperature is 31° C. An average OUR of 0.66 mmol O₂/(L·h) is recorded from 20 hours elapsed fermentation time (EFT) to the end of fermentation (40 hours EFT), and the vessels are run until free dextrose concentrations are 0.2-0.5 (40 hours EFT). The data represents the average of three independent fermentation vessels per strain.

The starting dextrose concentration is cross validated using a carbohydrate column (87C) to determine the free dextrose, DP2, DP3 and DP4+ concentrations in the T0+ samples and are multiplied by their respective chemical gain factors to determine the dextrose sum. This method is cross validated using an enzymatic hydrolysis method. Dextrose sum results are averaged for each vessel.

As shown in Table 20, strain 1-62 (having an exogenous lactate-consumption pathway) demonstrates a significantly higher ethanol titer and lactate consumption, and also shows significantly lower glycerol generation, than the reference strain.

TABLE 20 SSF batch fermenter data for strain 1-10 vs. strain 1-62 Starting Concentration (n = 3) Average Final Titer @ 40 hours (n = 3) Total Total Dextrose Glycerol Lactate Ethanol Dextrose Glycerol Lactate Ethanol (g/Kg) (g/Kg) (g/Kg) (g/kg) (g/Kg) (g/Kg) (g/Kg) (g/kg) Strain 1-10 256.6 ± 2.8 2.0 ± 0.3 6.6 ± 0.8 0.2 ± 0.0 0.6 ± 0.3 10.4 ± 0.5 5.6 ± 0.7   111 ± 1.2 Strain 1-62 254.8 ± 1.5 2.0 ± 0.3 6.6 ± 0.8 0.2 ± 0.1 0.9 ± 0.5  8.8 ± 0.4 4.4 ± 0.7 114.4 ± 0.2

Exemplary Embodiments

The embodiments in this section are designated sequentially with letters A through Z, then AA through AZ, then BA, and so on.

A. A genetically modified yeast comprising a heterologous gene encoding a monocarboxylic/monocarboxylate transporter and one or more heterologous genes encoding lactate dehydrogenase (cytochrome) (classified as EC 1.1.2.3 or 1.1.2.4), wherein the yeast is capable of consuming lactate and producing ethanol when the yeast is present in a fermentation medium comprising lactate and hexose.

B. The yeast of embodiment A, wherein the yeast has a L-lactate consumption rate of at least 0.030 0.035, 0.040, 0.045, or 0.050 gL⁻¹h⁻¹ when the concentration of hexose in the fermentation medium is 150 g/L or greater at a sampling time of 21 h, as measured according to the Evaluation Protocol for Lactate Consumption.

C. The yeast of embodiment A, wherein the yeast has a L-lactate consumption rate of at least 0.015, 0.020, 0.025, 0.030, 0.035, or 0.040 gL⁻¹h⁻¹ when the concentration of hexose in the fermentation medium is 5 g/L or greater at a sampling time of 48 h, as measured according to the Evaluation Protocol for Lactate Consumption.

D. The yeast of embodiment A, wherein the yeast has a D-lactate consumption rate of at least 0.005, 0.006, 0.007, 0.008, 0.009, 0.010, 0.015, 0.020, 0.025, or 0.030 gL⁻¹h⁻¹ when the concentration of hexose in the fermentation medium is 150 g/L or greater at a sampling time of 21 h, as measured according to the Evaluation Protocol for Lactate Consumption.

E. The yeast of embodiment A, wherein the yeast has a D-lactate consumption rate of at least 0.015, 0.020, 0.025, 0.030, 0.035, or 0.040 gL⁻¹h⁻¹ when the concentration of hexose in the fermentation medium is 5 g/L or greater at a sampling time of 48 h, as measured according to the Evaluation Protocol for Lactate Consumption.

F. The yeast of any of embodiments A-E, wherein the D-, L-, and/or total lactate consumption rate of the yeast is greater than a yeast without a heterologous gene encoding a monocarboxylic/monocarboxylate transporter.

G. The yeast of embodiment A, wherein the yeast has a total lactate consumption rate of at least 0.550, 0.555, 0.600 or 0.650 gL⁻¹h⁻¹ between time 0 and 7 hours in a simultaneous saccharification fermentation (SSF) process.

H. The yeast of embodiment A, wherein the yeast has a total lactate consumption rate of at least 0.130, 0.140, 0.150, 0.160, or 0.170 gL⁻¹h⁻¹ between time 7 hours and 48 hours in a SSF process.

I. The yeast of embodiment A, wherein the yeast has a total lactate consumption rate of at least 0.200, 0.210, 0.220, 0.230, 0.240, or 0.250 gL⁻¹h⁻¹ between time 0 and 48 hours in a SSF process.

J. The yeast of any of embodiments G-I, wherein the total lactate consumption rate is determined according to the method for SSF shake flask assay in Example 5.

K. The yeast of any of embodiments A-J, wherein the yeast is capable of consuming D-lactate, L-lactate, or a mixture thereof.

L. The yeast of any of embodiments A-K, wherein the one or more heterologous lactate dehydrogenase (cytochrome) genes comprise an overexpressed D-lactate dehydrogenase (DLD) gene.

M. The yeast of any of embodiments A-K, wherein the one or more heterologous lactate dehydrogenase (cytochrome) genes comprise an overexpressed cytochrome b2 (CYB2) gene.

N. The yeast of any of embodiments A-K, wherein the one or more heterologous lactate dehydrogenase (cytochrome) genes comprise an overexpressed DLD gene and an overexpressed CYB2 gene.

O. The yeast of any of embodiments L-N, wherein the one or more DLD genes is from one or more of the following yeast species: Saccharomyces cerevisiae, Issatchenkia orientalis, Saccharyomyces kluyveri, Saccharyomyces bayanus, Kluyveromyces dobzhanskii, Kluyveromyces marxianus, or Kluyveromyces lactis.

P. The yeast of any of embodiments A-O, wherein the yeast encodes for a polypeptide having an amino acid sequence with a sequence identity of at least 50%, 55%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, or 99% to any one of the following amino acid sequences: SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 72, or SEQ ID NO: 74.

Q. The yeast of any of embodiments M-N, wherein the one or more CYB2 genes is from one or more of the following yeast species: Saccharomyces cerevisiae, Issatchenkia orientalis, Saccharyomyces kluyveri, Saccharyomyces bayanus, Zygosaccharomyces rouxii, Kluyveromyces dobzhanskii, or Kluyveromyces lactis.

R. The yeast of any of embodiments A-Q, wherein the yeast encodes for a polypeptide having an amino acid sequence with a sequence identity of at least 50%, 55%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, or 99% to any one of the following amino acid sequences: SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, or SEQ ID NO: 62.

S. The yeast of any of embodiments A-R which comprises a heterologous gene encoding a lactate racemase.

T. A genetically modified yeast comprising a heterologous gene encoding a monocarboxylate/proton symporter and a heterologous gene encoding a glucoamylase, wherein the yeast is capable of consuming lactate and producing ethanol when the yeast is present in a fermentation medium comprising lactate and hexose, starch, or a combination of hexose and starch.

U. The yeast of any of embodiments A-T, wherein the yeast encodes for a glucoamylase from Saccharomycopsis fibuligera or Rhizopus oryzae.

V. The yeast of any of embodiments A-U, wherein the yeast is of the genus Saccharomyces.

W. The yeast of embodiment V, wherein the yeast is of the species Saccharomyces cerevisiae.

X. A genetically modified yeast comprising a yeast of the species Saccharomyces cerevisiae, wherein the yeast comprises a heterologous gene encoding a monocarboxylate/proton symporter.

Y. The yeast of embodiment X, wherein the yeast is obtained by genetically modifying a Saccharomyces cerevisiae host yeast and wherein the host yeast is ETHANOL RED™ (commercially available from Lesaffre).

Z. The yeast of any of embodiments A-Y which is capable of producing ethanol at a fermentation production rate of at least 1.0 g L⁻¹h⁻¹, 2.0 g L⁻¹h⁻¹, 3.0 g L⁻¹h⁻¹, 3.3 g L⁻¹h⁻¹, or 3.75 g L⁻¹h⁻¹.

AA. The yeast of any of embodiments A-Z which is capable of producing ethanol at a titer greater than 80 g/L, 90 g/L, 100 g/L, 110 g/L, 120 g/L, 125 g/L 130 g/L, 135 g/L, 140 g/L, 145 g/L, 150 g/L, 155 g/L, 160 g/L, or 165 g/L.

AB. The yeast of any of embodiments A-AA (i.e., A-Z and AA) which is (a) capable of producing ethanol at a titer of greater than 90 g/L, 100 g/L, 110 g/L, 120 g/L, 130 g/L, or 140 g/L; (b) thermotolerant at temperatures in the range of 33° C. to 40° C., 33° C. to 39° C., 33° C. to 38° C., 33° C. to 37° C., 34° C. to 37° C., 35° C. to 37° C., or 36° C. to 38° C.; or both (a) and (b).

AC. The yeast of any of embodiments A-AB, wherein the heterologous gene encoding a monocarboxylic/monocarboxylate transporter is from a yeast of the genus Kluyveromyces.

AD. The yeast of any of embodiments A-AC, wherein the heterologous gene encoding a monocarboxylic/monocarboxylate transporter is from Kluyveromyces lactis.

AE. The yeast of any of embodiments A-AD, wherein the yeast encodes for a polypeptide having an amino acid sequence with a sequence identity of at least 50%, 55%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, or 99% to any one of the following amino acid sequences: SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 76, or SEQ ID NO: 78.

AF. The yeast of embodiment AE, comprising one or more of the following residues at the indicated positions in SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, or SEQ ID NO: 62: Lys349, Tyr143, Tyr254, and His373.

AG. Use of the yeast of any of embodiments A-AF for the production of ethanol or a bioproduct other than ethanol.

AH. A process for producing ethanol comprising fermenting a substrate with the yeast of any of embodiments A-AG.

AI. A continuous fermentation process for manufacturing ethanol comprising: providing a fermentation medium comprising hexose or hexose oligomers, fermenting the fermentation medium with a genetically modified yeast comprising a heterologous monocarboxylate/proton symporter (JEN1) gene, adding one or more feed streams comprising lactate to the fermentation medium, and removing at least one output stream comprising ethanol from the fermentation medium, wherein the average hexose or hexose oligomer concentration of the fermentation medium is at least 5 g/L, the volumetric oxygen uptake rate of the process is at least 0.5 mmol O₂/(L·h), and the process produces ethanol at an overall rate of at least 1.0 g L⁻¹h⁻¹, and the yeast consumes lactate, wherein the at least one output stream contains less than 90% of the lactate added in the one or more feed streams.

AJ. The process of embodiment AI, wherein lactate concentration of one or more feed streams has an average lactate concentration of at least 1 g/L.

AK. The process of any of embodiments AI-AJ, wherein the feed stream is a vegetable process stream.

AL. The process of embodiment AK, wherein the vegetable process stream is a corn process stream or a wheat process stream.

AM. The process of any of embodiments AH-AL, wherein the ethanol titer at the end of the pre-fermenter step is in the range of 20 to 80 g/L.

AN. The process of any of embodiments AH-AM, wherein the L-lactate consumption rate in the propagator step or pre-fermenter step is at least 0.030 0.035, 0.040, 0.045, or 0.050 gL⁻¹h⁻¹.

AO. The process of any of embodiments AH-AN, wherein the D-lactate consumption rate in the propagator step or pre-fermenter step 0.005, 0.006, 0.007, 0.008, 0.009, 0.010, 0.015, 0.020, 0.025, or 0.030 gL⁻¹h⁻¹.

AP. The process of any of embodiments AH-AO, wherein the ethanol titer of the at least one output stream is at least 90, 100, 110, 120, 130, 140, 150, or 160 g/L.

AQ. A process for manufacturing ethanol comprising: fermenting a medium using a genetically modified yeast comprising a heterologous monocarboxylate/proton symporter gene, wherein the medium comprises glucose or glucose oligomers at a concentration of at least 5 g/L at the start of fermentation, the lactate content of the medium is at least 1 g/L at the start of fermentation, at least 40% of the lactate is consumed at the end of fermentation, and the final ethanol titer is at least 90 g/L.

AR. The process of any of embodiments AH-AQ, having a volumetric oxygen uptake rate (OUR) of at least 0.5, 1, 2, 3, or 4 mmol O₂/(L·h).

AS. A process for manufacturing ethanol comprising: fermenting a medium using a S. cerevisiae yeast, wherein the medium comprises glucose or glucose oligomers and lactate, the OUR is at least 0.5 mmol O₂/(L·h), the lactate content of the medium is at least 1 g/L at the start of fermentation, at least 35% of the lactate present in the medium at the start of fermentation and/or added to the medium during fermentation is consumed by the end of fermentation, and the final ethanol titer is at least 90 g/L.

AT. The process of embodiment AS, wherein the OUR is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 mmol O₂/(L·h).

AU. The process of any of embodiments AS-AT, wherein the lactate content of the medium is at least 2, 3, 4, or 5 g/L at the start of fermentation.

AV. The process of any of embodiments AS-AU, wherein at least 40, 45, or 50% of the lactate present in the medium at the start of fermentation and/or added to the medium during fermentation is consumed by the end of fermentation

AW. The process of any of embodiments AH-AV, wherein the yeast is the yeast of any of embodiments A-Y.

AX. The process of any of embodiments AH-AW, wherein the lactate is L-lactate, D-lactate, or a mixture thereof.

AY. The process of any of embodiments AH-AX, wherein the pH of the fermentation medium is in the range of about 2 to 7.

AZ. The process of any of embodiments AH-AY, wherein the fermentation temperature is in the range of 25 to 45° C., 25 to 40° C., 25 to 35° C., 30 to 40° C., or 28 to 38° C.

BA. The process of any of embodiments AH-AZ, wherein the dry solids of the fermentation medium is at least 30, 40, 50, 60, 70, or 80 g/L

BB. The process of any of embodiments AH-BA, wherein the dry solids of the fermentation feed is in the range of 120 to 150 g/L.

BC. The process of any of embodiments AH-BB, wherein the ethanol titer at the end of fermentation is at least 80, 90, 100, 110, 120, 130, 135, 140, 145, 150, 155, or 160 g/liter.

BD. A method for producing a genetically modified yeast with improved lactate consumption comprising overexpressing one or more heterologous genes encoding a lactate dehydrogenase (cytochrome) (classified as EC 1.1.2.3 or 1.1.2.4) or a heterologous monocarboxylate/proton symporter, and subjecting the yeast to evolution for a characteristic, wherein the yeast is capable of consuming lactate and producing ethanol when the yeast is present in a fermentation medium comprising lactate and glucose.

BE. The method of embodiment BD, wherein the characteristic is increased growth rate on lactate.

BF. The process or method of any of embodiments AH-BE, wherein the yeast encodes for a polypeptide having an amino acid sequence with a sequence identity of at least 50%, 55%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, or 99% to any one of the following amino acid sequence: SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 76, or SEQ ID NO: 78.

BG. The process or method of embodiment BF, wherein the yeast comprises one or more of the following residues at the indicated positions in SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, or SEQ ID NO: 62: Lys349, Tyr143, Tyr254, and His373.

BH. The process, method, or yeast of any of embodiments A-BG, wherein the yeast comprises a heterologous nucleic acid regulatory sequence.

BI. The process, method, or yeast of embodiment BH, wherein the heterologous nucleic acid regulatory sequence is associated with the heterologous gene encoding a monocarboxylic/monocarboxylate transporter.

BJ. The process, method, or yeast of embodiments BH or BI, wherein the heterologous nucleic acid regulatory sequence comprises the ADH1 promoter.

BK. The process, method, or yeast of embodiments BH or BI, wherein the heterologous nucleic acid regulatory sequence comprises the ADH2 promoter, the PDC1 promoter, or the GPD1 promoter.

It is also to be understood that the elements or aspects of any of the above embodiments of the processes, methods, or compositions described above can be applied to any other embodiment, even if not explicitly stated herein.

The disclosures of each and every patent, patent application, or publication cited herein are hereby incorporated by reference in their entirety. While this invention has been disclosed with reference to specific embodiments, other embodiments and variations of this invention may be devised by others skilled in the art without departing from the true spirit and scope of the invention. The appended claims are intended to be construed to include all such embodiments and variations. 

1. A genetically modified yeast comprising: a heterologous gene encoding a polypeptide with monocarboxylic/monocarboxylate transporter activity; one or more heterologous genes encoding a polypeptide with D-lactate dehydrogenase (DLD) activity; and one or more heterologous genes encoding a polypeptide with lactate dehydrogenase cytochrome b2 (CYB2) activity; wherein the yeast is capable of consuming lactate and producing ethanol at a titer greater than 80 g/L when the yeast is present in a fermentation medium comprising lactate and hexose.
 2. The yeast of claim 1, wherein the yeast has a L-lactate consumption rate of at least 0.015 gL⁻¹h⁻¹ when the concentration of hexose in the fermentation medium is 5 g/L or greater at a sampling time of 48 h, as measured according to the Evaluation Protocol for Lactate Consumption.
 3. The yeast of claim 1, wherein the yeast has a D-lactate consumption rate of at least 0.015 gL⁻¹h⁻¹ when the concentration of hexose in the fermentation medium is 5 g/L or greater at a sampling time of 48 h, as measured according to the Evaluation Protocol for Lactate Consumption.
 4. The yeast of claim 1, wherein the D-, L-, and/or total lactate consumption rate of the yeast is greater than a yeast without a heterologous gene encoding a polypeptide with monocarboxylic/monocarboxylate transporter activity.
 5. The yeast of claim 1, wherein the yeast is capable of consuming both D-lactate and L-lactate when the yeast is present in a fermentation medium comprising lactate and hexose.
 6. (canceled)
 7. (canceled)
 8. The yeast of claim 1, wherein the amino acid sequence of the DLD polypeptide has a sequence identity of at least 85% to any one of the following amino acid sequences: SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 72, or SEQ ID NO:
 74. 9. The yeast of claim 1, wherein the amino acid sequence of the CYB2 polypeptide has a sequence identity of at least 85% to any one of the following amino acid sequences: SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, or SEQ ID NO:
 62. 10. (canceled)
 11. The yeast of claim 1, wherein the yeast additionally comprises a heterologous gene encoding a polypeptide with glucoamylase activity and at least 80% sequence identity to the wild-type glucoamylase polypeptide from Saccharomycopsis fibuligera or Rhizopus oryzae.
 12. The yeast of claim 1, wherein the yeast is genetically modified from a host yeast of the species Saccharomyces cerevisiae.
 13. (canceled)
 14. The yeast of claim 1, wherein the yeast is capable of producing ethanol at a titer greater than 100 g/L.
 15. (canceled)
 16. The yeast of claim 1, wherein the amino acid sequence of the monocarboxylic/monocarboxylate transporter polypeptide has a sequence identity of at least 85% to any one of the following amino acid sequences: SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 76, or SEQ ID NO:
 78. 17. (canceled)
 18. A process for producing ethanol comprising fermenting a substrate with the yeast of claim
 1. 19. The process of claim 18, having a volumetric oxygen uptake rate (OUR) of at least 0.5 mmol O₂/(L·h).
 20. The process of claim 18, wherein the ethanol titer at the end of fermentation is at least 100 g/liter.
 21. A genetically modified yeast comprising: a heterologous gene encoding a polypeptide with monocarboxylic/monocarboxylate transporter activity; and a heterologous gene encoding a polypeptide with lactate dehydrogenase activity having a sequence identity of at least 85% to any one of the following amino acid sequences: SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, or SEQ ID NO: 62, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 72, and SEQ ID NO: 74 wherein the yeast is capable of consuming lactate and producing ethanol at a titer greater than 80 g/L when the yeast is present in a fermentation medium comprising lactate and hexose.
 22. The yeast of claim 21, wherein the polypeptide with lactate dehydrogenase activity comprises one or more residue selected from the group consisting of Lys349, Tyr143, Tyr254, and His373 at the indicated positions in at least one of SEQ ID NO: 15, SEQ ID NO: 17, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 58, SEQ ID NO: 60, or SEQ ID NO: 62
 23. The yeast of claim 21, wherein the amino acid sequence of the monocarboxylic/monocarboxylate transporter polypeptide has a sequence identity of at least 85% to any one of the following amino acid sequences: SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 76, or SEQ ID NO:
 78. 24. The yeast of claim 21, wherein the yeast is genetically modified from a host yeast of the species Saccharomyces cerevisiae.
 25. The yeast of claim 21, wherein the yeast additionally comprises a heterologous gene encoding a polypeptide with glucoamylase activity and at least 80% sequence identity to the wild-type glucoamylase polypeptide from Saccharomycopsis fibuligera or Rhizopus oryzae.
 26. The yeast of claim 21, wherein the yeast is capable of consuming both D-lactate and L-lactate when the yeast is present in a fermentation medium comprising lactate and hexose. 